| Full gene name: | cyclin-dependent kinase inhibitor 2A |
|---|---|
| Entrez Gene ID: | 1029 |
| Location: | 9p21 |
| Synonyms: | MTS-1, P16INK4A, ARF, P19ARF, CDKN2, MTS1, INK4, TP16, P16-INK4A, MLM, P14, CMM2, P16, P19, P14ARF, CDK4I, INK4A, P16INK4 |
| Type: | protein-coding |
SNPs given by the user that are near or inside this gene:
| SNP | Distance (bp) | Direction |
|---|---|---|
| rs10811661 | 139604 | upstream |
This gene generates several transcript variants which differ in their first exons. At least three alternatively spliced variants encoding distinct proteins have been reported, two of which encode structurally related isoforms known to function as inhibitors of CDK4 kinase. The remaining transcript includes an alternate first exon located 20 Kb upstream of the remainder of the gene; this transcript contains an alternate open reading frame (ARF) that specifies a protein which is structurally unrelated to the products of the other variants. This ARF product functions as a stabilizer of the tumor suppressor protein p53 as it can interact with, and sequester, MDM1, a protein responsible for the degradation of p53. In spite of the structural and functional differences, the CDK inhibitor isoforms and the ARF product encoded by this gene, through the regulatory roles of CDK4 and p53 in cell cycle G1 progression, share a common functionality in cell cycle G1 control. This gene is frequently mutated or deleted in a wide variety of tumors, and is known to be an important tumor suppressor gene. [provided by RefSeq, Jul 2008]
| OMIM ID: | `OMIM ID 600160 `_ |
|---|
Allelic Variants (Selected Examples)
.0001 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Among the melanoma (155601) cell lines that carried at least 1 copy of CDKN2A (the other copy frequently being deleted), Kamb et al. (1994) identified a variety of nonsense, missense, or frameshift mutations. One of these was a G-to-A transition that converted gly259 to ser.
.0002 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Among 14 melanoma (155601) cell lines in which at least 1 copy of CDKN2A was present (the other copy frequently being deleted) and in which nonsense, missense, or frameshift mutations were identified, Kamb et al. (1994) found the same mutation in 2: a C-to-T transition converting codon 232 from arg to stop.
.0003 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Gruis et al. (1995) analyzed CDKN2A coding sequences in 15 Dutch FAMMM syndrome pedigrees, and identified a 19-bp germline deletion in 13 of them. All 13 families originated from an endogamous population. The deletion caused a reading-frame shift, predicted to result in a severely truncated p16 protein. Homozygosity for the deletion was found in 2 family members, one of whom showed no obvious signs of melanoma. The finding demonstrated that homozygotes for this CDKN2A mutation are viable, and suggested the presence of a genetic mechanism that can compensate for the functional loss of p16. The results strengthened the notion that p16 is the molecular nature of the 9p21-linked form of familial melanoma (CMM2; 155601). Of the 2 homozygous individuals, one was fully examined at the age of 54 and showed as the only possible sign of FAMMM 3 very mildly atypical nevi. Until her death from adenocarcinoma (site not stated) at the age of 55, this subject remained free of melanomas. The second homozygote, a nephew of the first, had a very large number of atypical moles at the age of 11; at the age of 15, an invasive melanoma was found.
(In addition to the 19-bp deletion of p16, which goes by the name of Leiden, there is at least one familial hypercholesterolemia Leiden (143890.0041), factor V Leiden (612309.0001), apoE3 Leiden (107741.0006), and a hemoglobin Leiden (141900.0156).)
Van der Velden et al. (1999) hypothesized that a tentative second tumor-related gene in 9p21 may also act as a modifier of melanoma risk conveyed by known CDKN2A mutations. To identify genetic modifiers for a known, ‘primary’ susceptibility gene, one would ideally need to study a large number of carriers of a single mutation in that primary gene. Dutch FAMMM families provided them with a unique opportunity for such studies, since the 19-bp founder deletion in exon 2 of the CDKN2A gene, p16-Leiden, segregated in most Dutch FAMMM families. The 36% cumulative incidence for melanoma in p16-Leiden carriers illustrated a high melanoma risk associated with this mutation but also suggested that environmental and/or genetic factors act as risk modifiers. Van der Velden et al. (1999) performed haplotype analysis for 9p21 using microsatellite markers in 6 p16-Leiden families originating from a founder population. In 2 families, p16-Leiden carriers shared an unexpectedly large founder haplotype (approximately 20 cM) around CDKN2A, mostly in the proximal direction. Melanoma-positive p16-Leiden carriers from these families showed this extensive proximal haplotype, compared with melanoma-negative p16-Leiden carriers from the same families. Additional p16-Leiden families less heavily affected with melanoma showed shorter haplotype sharing, excluding the region proximal of CDKN2A. The presence of a gene involved in melanoma susceptibility proximal to CDKN2A was corroborated by somatic deletions of 9p in tumors, which frequently did not include CDKN2A but a more proximal chromosomal region instead. The results provided a candidate region for further gene mapping in p16-negative 9p21-linked melanoma families and guided the search for risk modifiers in melanoma development.
Vasen et al. (2000) performed mutation analysis on 27 families with FAMMM syndrome and identified the CDKN2A-Leiden mutation (600160.0005) in 19 families. They identified 86 patients with melanoma, and the second most frequent cancer was pancreatic carcinoma, which was observed in 15 patients from 7 families. The mean age at diagnosis of pancreatic carcinoma was 58 years, with a range from 38 to 77 years. Putative mutation carriers had an estimated cumulative risk of 17% for developing pancreatic carcinoma by age 75 years. In the 8 CDKN2A-Leiden-negative families, no cases of pancreatic carcinoma had occurred. The authors concluded that individuals with the CDKN2A-Leiden mutation show an enormous risk of developing pancreatic cancer (see 606719).
Schneider-Stock et al. (2003) found the p16-Leiden mutation in heterozygous state in the blood and all 3 tumors of a man who was diagnosed at age 54 years with simultaneous development of 3 carcinomas of the pharynx and oral cavity. The patient neither smoked more than 5 cigarettes daily nor abused alcohol. Both his parents and his only sister died of cancer very early (the mother of gynecologic cancer, the father of liver carcinoma, and the sister of leukemia).
.0004 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In a family with melanoma (155601), Liu et al. (1995) found an in-frame deletion of 2 amino acids, asp96 and leu97, in 3 affected and 2 unaffected members. The mutation was a 6-bp deletion of nucleotides 363-368 of their CDKN2A sequence.
.0005 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In 3 families with melanoma (155601), Hussussian et al. (1994) identified a gly93-to-trp mutation in the CDKN2A gene. (The GLY93TRP mutation is now designated GLY101TRP.)
Whelan et al. (1995) described a kindred with an increased risk of pancreatic cancers, melanomas, and possibly additional types of tumors (see 606719) cosegregating with the gly93-to-trp CDKN2 mutation. Of interest was the occurrence of squamous-cell carcinomas in this family, a rare form, and squamous cell carcinoma of the tongue in the proband. More than half of primary esophageal squamous cell carcinomas have CDKN2 mutations (Mori et al., 1994). The mutation was identified by SSCP analysis and was located in exon 2 where direct sequencing demonstrated a G-to-T nucleotide change at position 295.
Ciotti et al. (1996) indicated that in a small geographic area of Italy (possibly because of founder effect), they had detected the gly93-to-trp mutation in 7 apparently unrelated families and in none of 50 control persons. Nineteen cases of melanoma and 3 of dysplastic nevi were diagnosed at ages ranging from 21 to 70 years in the kindreds with the G93W mutation. In addition, 15 cancers at other sites were found in these kindreds, including 3 pancreatic cancers but no gastric cancers. The pancreatic tumors developed in members of 3 different families at the ages of 48, 51, and 60 years.
Ciotti et al. (2000) stated that gly101-to-trp is the most common CDKN2A missense mutation, having been reported in numerous families from around the world, with a particularly high occurrence in France and Italy. They examined the date of origin of the mutation and its migratory spread in 10 families from Italy, 4 families from the U.S., and 6 families from France. In all families studied, the mutation appeared to have been derived from a single ancestral haplotype. Using maximum likelihood methods, they estimated that the mutation arose 97 generations ago, providing some explanation for the wide geographic spread of this common mutation, particularly in southwestern Europe. All of the Italian families, with one exception, came from a small area on the eastern coast of Liguria.
Auroy et al. (2001) found the G101W mutation in 7 patients with multiple primary melanomas with no known melanoma cases within their families. They stated that the mutation had already been described in more than 20 melanoma-prone families. They genotyped 8 microsatellite markers flanking the CDKN2A gene and found, after allowing for recombination over time, that haplotype sharing provided evidence for an original G101W mutation common to 6 of the 7 sporadic multiple primary melanoma cases.
In Italy, Mantelli et al. (2002) screened for CDKN2A mutations in families with 2 melanoma patients, 1 of whom was younger than 50 years at onset and the other complying with 1 of the following: being a first-degree relative; having an additional relative with pancreatic cancer; or having multiple primary melanomas. Mutations were found in 21 of the 62 families (34%) with a high prevalence of the G101W mutation (18 of 21).
.0006 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO , 2
In 10 melanoma (155601) kindreds from southern Sweden, Borg et al. (1996) identified a novel germline mutation in 2 families, constituting an in-frame 3-bp duplication at nucleotide 332 in exon 2. The mutation resulted in an insertion of arg at codon 105, which interrupts the last of the 4 ankyrin repeats of the p16 protein, motifs which have been demonstrated as important in binding and inhibiting the activity of cyclin D-dependent kinases 4 and 6 in cell cycle G1 phase regulation. Other malignancies observed in gene carriers or obligate carriers included cervical, breast, and pancreatic carcinomas, and a non-Hodgkin lymphoma. Analysis of microsatellite markers adjacent to the p16 gene at chromosomal region 9p21 in the 2 families with the mutation showed that they shared a common haplotype, in keeping with a common ancestor.
By haplotype analysis, Hashemi et al. (2001) concluded that the mutation arose 98 generations, or approximately 2,000 years, ago. Thus, the mutation, which they designated 113insR, could be expected to have a more widespread geographic distribution in regions of Europe and North America with ancestral connections to Sweden. Alternatively, CDKN2A may lie in a recombination hotspot region, as suggested by the finding of many meiotic recombinations in a narrow region of approximately 1 cM on 9p21.
.0007 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Harland et al. (1997) identified a met53-to-ile (M53I) mutation in the CDKN2A gene in affected members of a family with melanoma (155601). They showed that the protein expressed from this previously described mutation did not bind to CDK4/CDK6 (see 123829), confirming its role as a causal mutation in melanoma. Monzon et al. (1998) found the same mutation in a patient with multiple melanomas who was thought to have no family history of melanoma when first investigated.
Pollock et al. (1998) pointed out that the M53I mutation had been described in 5 melanoma families from Australia and North America. Haplotype analysis suggested that there may have been only 1 original M53I mutation.
MacKie et al. (1998) identified this mutation in 4 U.K. melanoma families and also in 1 patient with multiple primary melanomas and a negative family history.
.0008 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In a patient with multiple primary melanomas (155601), Monzon et al. (1998) identified an arg24-to-pro mutation in the CDKN2A gene. They pointed out that this mutation had previously been reported in melanoma-prone families and was found to cosegregate with cases of melanoma. MacKie et al. (1998) identified this mutation in a U.K. melanoma family.
.0009 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Pollock et al. (1998) identified 2 new melanoma (155601) kindreds that carried a duplication of a 24-bp repeat present in the 5-prime region of the CDKN2A gene. This brought to a total of 5 the number of melanoma families described with this mutation; the 5 families were from 3 continents: Europe, North America, and Australasia. Previous families were reported by Goldstein et al. (1995), Walker et al. (1995), and Flores et al. (1997). This suggested to Pollock et al. (1998) that there had been at least 3 independent 24-bp duplication events. The duplication was hypothesized to have arisen due to an unequal crossing-over between the two 24-bp repeats naturally present in the wildtype sequence, possibly through polymerase slippage during replication. Further evidence that this repeat region is unstable and therefore prone to both meiotic and mitotic slippage was provided by the identification of a somatic 24-bp deletion of 1 of these normally occurring repeats in a prostate tumor (Komiya et al., 1995).
.0010 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Though germline CDKN2A coding mutations cosegregated with melanoma (155601) in 25 to 60% of families predisposed to the disease, there remain a number of mutation-negative families that demonstrate linkage of inherited melanoma to 9p21 markers (Hayward, 1996). Liu et al. (1999) showed that a subset of these kindreds possesses a G-to-T transversion at nucleotide -34 of CDKN2A, designated -34G-T. The mutation gives rise to a novel AUG translation initiation codon that decreases translation from the wildtype AUG. The -34G-T mutation was not seen in controls, segregated with melanoma in families, and, on the basis of haplotyping studies, appeared to have arisen from a common founder in the United Kingdom. Liu et al. (1999) suggested that screening for mutations in the promoter region of the CDKN2A gene should be useful in English (MacGeoch et al., 1994), Australian (Holland et al., 1995), and other northern European populations (Borg et al., 1996) in which a low incidence of germline coding mutations of CDKN2A has been found in familial melanoma cases.
.0012 MELANOMA AND NEURAL SYSTEM TUMOR SYNDROME
Randerson-Moor et al. (2001) described a family characterized by multiple melanoma and neural cell tumors (155755) segregating with a germline deletion of the p14(ARF)-specific exon 1-beta of CDKN2A. The deletion was approximately 14 kb and did not affect the coding or minimal promoter sequences of either CDKN2A or CDKN2B.
.0013 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
One of the most common melanoma (155601)-related CDKN2A mutations reported in North America is val126 to asp (V126D). Goldstein et al. (2001) examined 9 markers surrounding the CDKN2A gene in 3 American and 4 Canadian families carrying this mutation. All 7 families had a haplotype consistent with a common ancestor/founder. The mutation appeared to have originated 34 to 52 generations ago; 1 lod unit supported an interval of 13 to 98 generations.
.0014 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Harland et al. (2001) reported that affected individuals in 6 of 90 English melanoma (155601) pedigrees screened carried a transition (IVS2-105 A-G) deep in intron 2 of the CDKN2A gene. The mutation creates a false GT splice donor site 105 bases 5-prime of exon 3 and results in aberrant splicing of the mRNA. The authors proposed that this mutation and others similar to it may account for a significant proportion of 9p21-linked melanoma pedigrees with no detectable mutations in the coding region of CDKN2A.
.0015 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Hewitt et al. (2002) reported a family harboring a splice mutation in exon 1-beta of the CDKN2A gene that resulted in ARF haploinsufficiency. The mutation was observed in a mother and daughter with melanoma and a sib of the mother with breast cancer. The mutation was a 334G-C transversion in exon 1-beta, which predicts a gly122-to-arg substitution. Its position at the 3-prime end of exon 1-beta raised the possibility of interference with splicing. Analysis of the melanoma from 1 individual revealed a 62-bp deletion in exon 3 of the wildtype allele and loss of the mutant allele; these somatic changes would affect both CDKN2A and ARF. The authors suggested that concomitant inactivation of both ARF and CDKN2A may be necessary for melanoma development and that mutations in ARF and CDKN2A possibly confer different levels of susceptibility to melanoma, with the former associated with lesser predisposition.
.0016 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
A val59-to-gly mutation in the CDKN2A gene was found in 4 families segregating cutaneous malignant melanoma (155601): an Israeli family of Moroccan Jewish ancestry (Yakobson et al., 2001), 2 French families (1 of Tunisian Jewish ancestry and another without known Jewish roots) (Soufir et al., 1998), and a Spanish family (Ruiz et al., 1999). Yakobson et al. (2003) found that all but 1 of those affected in these families were heterozygous for the mutation; 1 affected member of the Israeli family was homozygous. Haplotype analysis indicated a single ancestral founder. The mutation, which occurs in a hydrophobic region with the second ankyrin repeat, impairs p16-INK4a function, as shown by studies of protein-protein interactions and cell proliferation assays.
.0017 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In 4 affected members from 3 families and 1 isolated patient with cutaneous malignant melanoma (155601), Kannengiesser et al. (2007) identified a heterozygous tandem germline 339G-C transversion and 340C-T transition in the CDKN2A gene, resulting in a leu113-to-leu (L113L) and a pro114-to-ser (P114S) substitution, respectively. All families were from southeastern France, and haplotype analysis indicated a founder effect. The sporadic patient had a high sun exposure history and Parkinson disease (168600) and received treatment with levodopa. He subsequently developed 22 primary melanomas, suggesting that levodopa may have contributed to the lesions. Further testing of this individual showed 2 pathogenic variants in the MC1R gene (see, e.g., R151C; 155555.0004), which likely contributed to the severe phenotype.
.0018 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In affected members of 3 families with cutaneous malignant melanoma (155601), Kannengiesser et al. (2007) identified a 167G-T transversion in the CDKN2A gene, resulting in a ser56-to-ile (S56I) substitution. Two patients were homozygous for the mutation, suggesting remote consanguinity. All families were from southeastern France, and haplotype analysis indicated a founder effect.
.0019 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
Goldstein et al. (2008) identified a gly89-to-asp (G89D) variant in the CDKN2A gene that was associated with significantly increased risk for cutaneous malignant melanoma (155601) in an Icelandic population. The mutation results in a synonymous G143G change in the p14(ARF) protein. The frequency of the G89D variant was 0.7 in melanoma patients compared to 0.08 in controls. The association was strengthened when restricted to invasive melanoma, present in 2% of patients (p = 0.0015). Relatives of affected G89D carriers were at significantly increased risk of melanoma, head and neck cancers, and pancreatic carcinoma compared to relatives of other melanoma patients. Haplotype analysis indicated a founder effect. The common ancestor was determined to be a female who lived in Hunavatnssysla county in northern Iceland from about 1605-1665.
.0020 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In affected members of 2 unrelated Italian families with malignant melanoma (155601), Binni et al. (2010) identified a heterozygous A-to-G transition in exon 1B of the CDKN2A gene, affecting splicing of the p14(ARF) isoform. The families were ascertained from a large cohort of 155 Italian probands.
.0021 MELANOMA, CUTANEOUS MALIGNANT, SUSCEPTIBILITY TO, 2
In affected members of an Italian family with malignant melanoma (155601), Binni et al. (2010) identified a heterozygous 161G-A transition in exon 1B of the CDKN2A gene, resulting in an arg54-to-his (R54H) substitution in a highly conserved residue of the p14(ARF) isoform. The family was ascertained from a large cohort of 155 Italian probands.
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