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NM_001142800.2(EYS):c.8429C>T (p.Thr2810Ile) AND not specified

Germline classification:
Benign (2 submissions)
Last evaluated:
Mar 13, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000333936.6

Allele description [Variation Report for NM_001142800.2(EYS):c.8429C>T (p.Thr2810Ile)]

NM_001142800.2(EYS):c.8429C>T (p.Thr2810Ile)

Genes:
PHF3:PHD finger protein 3 [Gene - OMIM - HGNC]
EYS:eyes shut homolog [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q12
Genomic location:
Preferred name:
NM_001142800.2(EYS):c.8429C>T (p.Thr2810Ile)
HGVS:
  • NC_000006.12:g.63721602G>A
  • NG_023443.2:g.1990624C>T
  • NG_034034.2:g.90802G>A
  • NM_001142800.2:c.8429C>TMANE SELECT
  • NM_001290259.2:c.*7894G>A
  • NM_001292009.2:c.8492C>T
  • NM_001370348.2:c.*7894G>AMANE SELECT
  • NM_001370349.2:c.*7894G>A
  • NM_001370350.2:c.*7894G>A
  • NM_015153.4:c.*7894G>A
  • NP_001136272.1:p.Thr2810Ile
  • NP_001278938.1:p.Thr2831Ile
  • FM209056.1:c.8492C>T
  • NC_000006.11:g.64431498G>A
  • NM_001142800.1:c.8429C>T
Protein change:
T2810I
Links:
dbSNP: rs144513453
NCBI 1000 Genomes Browser:
rs144513453
Molecular consequence:
  • NM_001290259.2:c.*7894G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370348.2:c.*7894G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370349.2:c.*7894G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370350.2:c.*7894G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_015153.4:c.*7894G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001142800.2:c.8429C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001292009.2:c.8492C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000341024Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions 2015)		Benign
(Apr 13, 2016) 		germlineclinical testing

Citation Link,

SCV002500352Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(Mar 13, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

EYS is a major gene for rod-cone dystrophies in France.

Audo I, Sahel JA, Mohand-Saïd S, Lancelot ME, Antonio A, Moskova-Doumanova V, Nandrot EF, Doumanov J, Barragan I, Antinolo G, Bhattacharya SS, Zeitz C.

Hum Mutat. 2010 May;31(5):E1406-35. doi: 10.1002/humu.21249.

PubMed [citation]
PMID:
20333770

Details of each submission

From Eurofins Ntd Llc (ga), SCV000341024.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002500352.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: EYS c.8429C>T (p.Thr2810Ile) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00095 in 157414 control chromosomes, predominantly at a frequency of 0.015 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 4.4 fold of the estimated maximal expected allele frequency for a pathogenic variant in EYS causing Retinitis Pigmentosa phenotype (0.0034), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Although reported in the literature among EYS variants unlikely to be pathogenic in a cohort of individuals with sporadic or autosomal recessive Retinitis Pigmentosa (example, Audo_2010), to our knowledge, no penetrant association of c.8429C>T in individuals affected with Retinitis Pigmentosa and no experimental evidence demonstrating its impact on protein function have been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and a predominant consensus as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024