chr6:64431122:G>T Detail (hg19) (PHF3, EYS)

Information

Genome

Assembly Position
hg19 chr6:64,431,122-64,431,122
hg38 chr6:63,721,226-63,721,226 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001142800.1:c.8805C>A NP_001136272.1:p.Tyr2935Ter
NM_001292009.1:c.8868C>A NP_001278938.1:p.Tyr2956Ter
Ensemble ENST00000503581.6:c.8805C>A ENST00000503581.6:p.Tyr2935Ter
Type Transcript Protein
RefSeq NM_001290259.1:c.*7518G>T
Ensemble ENST00000262043.8:c.*7518G>T
Summary

MGeND

Clinical significance Pathogenic
Variant entry 21
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.003
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 612424 OMIM
HGNC 21555 HGNC
Ensembl ENSG00000188107 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv25589763 TogoVar
COSMIC COSM1187074 COSMIC
MONDO
Type Database ID Link
Gene MIM 607789 OMIM
HGNC 8921 HGNC
Ensembl ENSG00000118482 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv25589763 TogoVar
COSMIC COSM1187074 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic retinitis pigmentosa germline MGS000009
(TMGS000012) 		Shoji Tsuji Tokyo University
Pathogenic Cone-Rod Dystrophy germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Pathogenic other unknown MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2022-12-13 criteria provided, single submitter retinitis pigmentosa germline not provided Detail
Pathogenic 2023-12-13 criteria provided, single submitter not provided germline Detail
Pathogenic 2023-10-01 criteria provided, multiple submitters, no conflicts Retinal dystrophy germline Detail
Pathogenic Likely pathogenic 2023-10-21 criteria provided, multiple submitters, no conflicts retinitis pigmentosa 25 germline unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.370 retinitis pigmentosa NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter) AND Retinitis pigmentosa ClinVar Detail
NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter) AND not provided ClinVar Detail
NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter) AND Retinal dystrophy ClinVar Detail
NM_001142800.2(EYS):c.8805C>A (p.Tyr2935Ter) AND Retinitis pigmentosa 25 ClinVar Detail
NA 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
rs527236067 dbSNP
Genome
hg19
Position
chr6:64,431,122-64,431,122
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
189.91
Standard deviation of sample read depth (HGVD)
83.84
Number of reference allele (HGVD)
2413
Number of alternative allele (HGVD)
7
Allele Frequency (HGVD)
0.002892561983471074
Gene Symbol (HGVD)
EYS
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))
rs527236067
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0018
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
31
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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