chr3:14158387:G>A Detail (hg38) (XPC)

Information

Genome

Assembly Position
hg19 chr3:14,199,887-14,199,887 View the variant detail on this assembly version.
hg38 chr3:14,158,387-14,158,387

HGVS

Type Transcript Protein
RefSeq NM_004628.4:c.1496C>T NP_004619.3:p.Ala499Val
Ensemble ENST00000285021.12:c.1496C>T ENST00000285021.12:p.Ala499Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.323
ToMMo:0.336
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.358

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613208 OMIM
HGNC 12816 HGNC
Ensembl ENSG00000154767 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv11549696 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-08-27 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-12-05 criteria provided, multiple submitters, no conflicts Xeroderma pigmentosum, group C germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2023-07-07 criteria provided, single submitter xeroderma pigmentosum group A germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.084 Carcinoma of lung Furthermore, a significant effect of SNPs in nucleotide excision repair pathway ... BeFree 21739480 Detail
0.008 Carcinoma of lung Furthermore, a significant effect of SNPs in nucleotide excision repair pathway ... BeFree 21739480 Detail
0.067 Malignant neoplasm of lung Furthermore, a significant effect of SNPs in nucleotide excision repair pathway ... BeFree 21739480 Detail
0.044 Malignant neoplasm of lung Furthermore, a significant effect of SNPs in nucleotide excision repair pathway ... BeFree 21739480 Detail
0.085 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.008 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.015 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.011 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
0.002 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.009 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.019 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.001 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.004 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
0.018 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
0.023 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.013 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
0.002 breast carcinoma Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
0.098 Malignant neoplasm of breast Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... BeFree 18701435 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Triple Negative Breast Neoplasms Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R41... BeFree 25023197 Detail
<0.001 Squamous cell carcinoma of oropharynx These findings suggest that polymorphisms of XPC-rs2228000, XPD-rs1799793 and XP... BeFree 23335232 Detail
<0.001 Squamous cell carcinoma of oropharynx In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793... BeFree 23335232 Detail
<0.001 Squamous cell carcinoma of oropharynx In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793... BeFree 23335232 Detail
<0.001 Squamous cell carcinoma of oropharynx In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793... BeFree 23335232 Detail
0.569 XERODERMA PIGMENTOSUM, COMPLEMENTATION GROUP C Several polymorphisms (Lys(939)Gln, PAT+/- and Ala(499)Val) in the DNA nuclear e... BeFree 18771913 Detail
0.003 adenoma Smoking was related to adenoma risk and XPC polymorphisms (R492H, A499V, K939Q) ... BeFree 16492920 Detail
0.003 colorectal carcinoma Individuals with variant genotypes of XPC Ala499Val appeared to be associated wi... BeFree 25355595 Detail
0.007 colorectal cancer XPC Lys939Gln and Ala499Val polymorphisms in colorectal cancer susceptibility: a... BeFree 24385304 Detail
0.003 colorectal carcinoma XPC Lys939Gln and Ala499Val polymorphisms in colorectal cancer susceptibility: a... BeFree 24385304 Detail
0.006 Paroxysmal atrial tachycardia Numerous studies have investigated the association between three polymorphisms (... BeFree 23918308 Detail
0.032 Malignant neoplasm of urinary bladder Individuals homozygous for the variant allele of XPC c.1496C &gt; T (p.Ala499Val... BeFree 21689419 Detail
0.007 colorectal cancer Individuals with variant genotypes of XPC Ala499Val appeared to be associated wi... BeFree 25355595 Detail
<0.001 gallbladder adenocarcinoma Ala499Val (C&gt;T) and Lys939Gln (A&gt;C) polymorphisms of the XPC gene: their c... BeFree 21113018 Detail
0.006 Carcinoma of bladder Individuals homozygous for the variant allele of XPC c.1496C &gt; T (p.Ala499Val... BeFree 21689419 Detail
0.006 Paroxysmal atrial tachycardia This meta-analysis including 13 case-control studies evaluated the associations ... BeFree 23381646 Detail
0.006 Paroxysmal atrial tachycardia This meta-analysis shows that the XPC PAT and Ala499Val polymorphisms may be ass... BeFree 24338715 Detail
0.006 Paroxysmal atrial tachycardia The overall genotype and allelotype distributions of XPC intron 9 PAT(+/-) and e... BeFree 17653764 Detail
0.005 breast carcinoma We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.018 breast carcinoma We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.098 Malignant neoplasm of breast We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.002 breast carcinoma We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.026 Malignant neoplasm of breast We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
0.023 Malignant neoplasm of breast We evaluated associations between seven single-nucleotide polymorphisms in four ... BeFree 21622940 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004628.5(XPC):c.1496C>T (p.Ala499Val) AND not specified ClinVar Detail
NM_004628.5(XPC):c.1496C>T (p.Ala499Val) AND Xeroderma pigmentosum, group C ClinVar Detail
NM_004628.5(XPC):c.1496C>T (p.Ala499Val) AND not provided ClinVar Detail
NM_004628.5(XPC):c.1496C>T (p.Ala499Val) AND Xeroderma pigmentosum group A ClinVar Detail
Furthermore, a significant effect of SNPs in nucleotide excision repair pathway on lung cancer survi... DisGeNET Detail
Furthermore, a significant effect of SNPs in nucleotide excision repair pathway on lung cancer survi... DisGeNET Detail
Furthermore, a significant effect of SNPs in nucleotide excision repair pathway on lung cancer survi... DisGeNET Detail
Furthermore, a significant effect of SNPs in nucleotide excision repair pathway on lung cancer survi... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
Our results suggest that TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3... DisGeNET Detail
These findings suggest that polymorphisms of XPC-rs2228000, XPD-rs1799793 and XPG-rs17655 in the NER... DisGeNET Detail
In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793 and XPG-rs17655 wer... DisGeNET Detail
In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793 and XPG-rs17655 wer... DisGeNET Detail
In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793 and XPG-rs17655 wer... DisGeNET Detail
Several polymorphisms (Lys(939)Gln, PAT+/- and Ala(499)Val) in the DNA nuclear excision repair gene ... DisGeNET Detail
Smoking was related to adenoma risk and XPC polymorphisms (R492H, A499V, K939Q) modified these effec... DisGeNET Detail
Individuals with variant genotypes of XPC Ala499Val appeared to be associated with the increased ris... DisGeNET Detail
XPC Lys939Gln and Ala499Val polymorphisms in colorectal cancer susceptibility: a meta-analysis of ca... DisGeNET Detail
XPC Lys939Gln and Ala499Val polymorphisms in colorectal cancer susceptibility: a meta-analysis of ca... DisGeNET Detail
Numerous studies have investigated the association between three polymorphisms (Lys939Gln, Ala499Val... DisGeNET Detail
Individuals homozygous for the variant allele of XPC c.1496C &gt; T (p.Ala499Val) were shown in a la... DisGeNET Detail
Individuals with variant genotypes of XPC Ala499Val appeared to be associated with the increased ris... DisGeNET Detail
Ala499Val (C&gt;T) and Lys939Gln (A&gt;C) polymorphisms of the XPC gene: their correlation with the ... DisGeNET Detail
Individuals homozygous for the variant allele of XPC c.1496C &gt; T (p.Ala499Val) were shown in a la... DisGeNET Detail
This meta-analysis including 13 case-control studies evaluated the associations between three common... DisGeNET Detail
This meta-analysis shows that the XPC PAT and Ala499Val polymorphisms may be associated with an incr... DisGeNET Detail
The overall genotype and allelotype distributions of XPC intron 9 PAT(+/-) and exon 15 Lys939Gln and... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail
We evaluated associations between seven single-nucleotide polymorphisms in four DNA repair genes (ER... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2228000 dbSNP
Genome
hg38
Position
chr3:14,158,387-14,158,387
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
184.65
Standard deviation of sample read depth (HGVD)
81.04
Number of reference allele (HGVD)
1638
Number of alternative allele (HGVD)
782
Allele Frequency (HGVD)
0.3231404958677686
Gene Symbol (HGVD)
XPC
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2228000
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3359
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5630
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8596
East Asian Allele Counts (ExAC)
3074
East Asian Heterozygous Counts (ExAC)
1934
East Asian Homozygous Counts (ExAC)
570
East Asian Allele Frequency (ExAC)
0.3576081898557469
Chromosome Counts in All Race (ExAC)
120500
Allele Counts in All Race (ExAC)
28649
Heterozygous Counts in All Race (ExAC)
21273
Homozygous Counts in All Race (ExAC)
3688
Allele Frequency in All Race (ExAC)
0.23775103734439834
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