chr16:13947991:C>T Detail (hg38) (ERCC4)

Information

Genome

Assembly Position
hg19 chr16:14,041,848-14,041,848 View the variant detail on this assembly version.
hg38 chr16:13,947,991-13,947,991

HGVS

Type Transcript Protein
RefSeq NM_005236.2:c.2395C>T NP_005227.1:p.Arg799Trp
Ensemble ENST00000311895.8:c.2395C>T ENST00000311895.8:p.Arg799Trp
ENST00000682617.1:c.2533C>T ENST00000682617.1:p.Arg845Trp
Summary

MGeND

Clinical significance Uncertain significance not provided
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 133520 OMIM
HGNC 3436 HGNC
Ensembl ENSG00000175595 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv54823713 TogoVar
COSMIC COSM967199 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Uncertain significance 2020/08/16 small intestine, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
not provided Cerebellar ataxia germline MGS000058
(TMGS000101) 		Fumihiko Matsuda The Rare Disease Data Registry of Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2022-02-22 criteria provided, multiple submitters, no conflicts Xeroderma pigmentosum, group F germline maternal unknown Detail
Uncertain significance 2016-03-29 criteria provided, single submitter not specified germline Detail
Conflicting interpretations of pathogenicity 2024-03-01 criteria provided, conflicting interpretations not provided germline Detail
Pathogenic 2023-12-30 criteria provided, single submitter Xeroderma pigmentosum, group F,Fanconi anemia complementation group Q,Cockayne syndrome germline unknown Detail
Pathogenic 2023-12-30 criteria provided, single submitter Xeroderma pigmentosum, group F,Fanconi anemia complementation group Q,Cockayne syndrome germline unknown Detail
Pathogenic 2023-12-30 criteria provided, single submitter Xeroderma pigmentosum, group F,Fanconi anemia complementation group Q,Cockayne syndrome germline unknown Detail
Pathogenic 2019-04-04 no assertion criteria provided XFE progeroid syndrome germline Detail
Uncertain significance 2021-03-30 criteria provided, single submitter Xeroderma pigmentosum, group F,XFE progeroid syndrome,Fanconi anemia complementation group Q germline Detail
Uncertain significance 2021-03-30 criteria provided, single submitter Xeroderma pigmentosum, group F,XFE progeroid syndrome,Fanconi anemia complementation group Q germline Detail
Uncertain significance 2021-03-30 criteria provided, single submitter Xeroderma pigmentosum, group F,XFE progeroid syndrome,Fanconi anemia complementation group Q germline Detail
Likely pathogenic no assertion criteria provided Hutchinson-Gilford syndrome unknown Detail
Uncertain significance 2019-01-01 criteria provided, single submitter breast carcinoma unknown Detail
Likely pathogenic 2021-03-04 no assertion criteria provided Carcinoma of pancreas germline Detail
Uncertain significance 2021-03-04 criteria provided, single submitter Fanconi anemia complementation group Q unknown Detail
Likely pathogenic 2022-05-21 criteria provided, multiple submitters, no conflicts xeroderma pigmentosum germline Detail
Likely pathogenic 2024-02-22 criteria provided, single submitter ERCC4-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 xeroderma pigmentosum In an attempt to determine how mutations in XPF can lead to such diverse symptom... BeFree 20221251 Detail
<0.001 progeria In an attempt to determine how mutations in XPF can lead to such diverse symptom... BeFree 20221251 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Xeroderma pigmentosum, group F ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND not specified ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND not provided ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND XFE progeroid syndrome ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND multiple conditions ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Hutchinson-Gilford syndrome ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Breast carcinoma ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Carcinoma of pancreas ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Fanconi anemia complementation group Q ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND Xeroderma pigmentosum ClinVar Detail
NM_005236.3(ERCC4):c.2395C>T (p.Arg799Trp) AND ERCC4-related disorder ClinVar Detail
In an attempt to determine how mutations in XPF can lead to such diverse symptoms, the effects of a ... DisGeNET Detail
In an attempt to determine how mutations in XPF can lead to such diverse symptoms, the effects of a ... 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
rs121913049 dbSNP
Genome
hg38
Position
chr16:13,947,991-13,947,991
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
157.31
Standard deviation of sample read depth (HGVD)
73.75
Number of reference allele (HGVD)
2418
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.264462809917355E-4
Gene Symbol (HGVD)
ERCC4
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))
rs121913049
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0011
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
18
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.3126734505087883E-4
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
62
Heterozygous Counts in All Race (ExAC)
62
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
5.107168157630274E-4
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