chr16:14041848:C>T Detail (hg19) (ERCC4)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr16:14,041,848-14,041,848 |
| hg38 | chr16:13,947,991-13,947,991 View the variant detail on this assembly version. |
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
|
| Variant entry | 2 |
| 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 | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Uncertain significance
|
2018/05/23 | colon, unspecified |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Uncertain significance
|
2018/05/23 | other |
germline
|
MGS000029
(TMGS000133) |
Hitoshi Nakagama | National Cancer Center 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
| Descrption | Source | Links |
|---|---|---|
| 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
- hg19
- Position
- chr16:14,041,848-14,041,848
- 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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