chr6:63720822:A>G Detail (hg38) (PHF3, EYS)

Information

Genome

Assembly Position
hg19 chr6:64,430,718-64,430,718 View the variant detail on this assembly version.
hg38 chr6:63,720,822-63,720,822

HGVS

Type Transcript Protein
RefSeq NM_001292009.1:c.9272T>C NP_001278938.1:p.Ile3091Thr
NM_001142800.1:c.9209T>C NP_001136272.1:p.Ile3070Thr
Ensemble ENST00000370621.7:c.9272T>C ENST00000370621.7:p.Ile3091Thr
Type Transcript Protein
RefSeq NM_001290259.1:c.*7114A>G
Ensemble ENST00000262043.8:c.*7114A>G
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
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 tgv25589742 TogoVar
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 tgv25589742 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other unknown MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2017-04-27 criteria provided, single submitter retinitis pigmentosa germline not provided Detail
Benign 2024-01-30 criteria provided, single submitter not provided germline Detail
Uncertain significance 2023-08-04 criteria provided, single submitter not specified germline Detail
Likely benign 2023-10-01 criteria provided, single submitter Retinal dystrophy germline 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.9209T>C (p.Ile3070Thr) AND Retinitis pigmentosa ClinVar Detail
NM_001142800.2(EYS):c.9209T>C (p.Ile3070Thr) AND not provided ClinVar Detail
NM_001142800.2(EYS):c.9209T>C (p.Ile3070Thr) AND not specified ClinVar Detail
NM_001142800.2(EYS):c.9209T>C (p.Ile3070Thr) AND Retinal dystrophy 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
rs183589498 dbSNP
Genome
hg38
Position
chr6:63,720,822-63,720,822
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
201.66
Standard deviation of sample read depth (HGVD)
88.89
Number of reference allele (HGVD)
2413
Number of alternative allele (HGVD)
5
Allele Frequency (HGVD)
0.0020678246484698098
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))
rs183589498
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
33
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
622
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.003215434083601286
Chromosome Counts in All Race (ExAC)
21946
Allele Counts in All Race (ExAC)
3
Heterozygous Counts in All Race (ExAC)
3
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.366991706916978E-4
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