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NM_001142800.2(EYS):c.9380_9399del (p.Ile3127fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 15, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001009220.1

Allele description [Variation Report for NM_001142800.2(EYS):c.9380_9399del (p.Ile3127fs)]

NM_001142800.2(EYS):c.9380_9399del (p.Ile3127fs)

Genes:
PHF3:PHD finger protein 3 [Gene - OMIM - HGNC]
EYS:eyes shut homolog [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
6q12
Genomic location:
Preferred name:
NM_001142800.2(EYS):c.9380_9399del (p.Ile3127fs)
HGVS:
  • NC_000006.12:g.63720632_63720651del
  • NG_023443.2:g.1991575_1991594del
  • NG_034034.2:g.89832_89851del
  • NM_001142800.2:c.9380_9399delMANE SELECT
  • NM_001290259.2:c.*6924_*6943del
  • NM_001292009.2:c.9443_9462del
  • NM_001370348.2:c.*6924_*6943delMANE SELECT
  • NM_001370349.2:c.*6924_*6943del
  • NM_001370350.2:c.*6924_*6943del
  • NM_015153.4:c.*6924_*6943del
  • NP_001136272.1:p.Ile3127fs
  • NP_001278938.1:p.Ile3148fs
  • NC_000006.11:g.64430528_64430547del
  • NM_001142800.1:c.9380_9399del20
Protein change:
I3127fs
Links:
dbSNP: rs1582139086
NCBI 1000 Genomes Browser:
rs1582139086
Molecular consequence:
  • NM_001290259.2:c.*6924_*6943del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370348.2:c.*6924_*6943del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370349.2:c.*6924_*6943del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001370350.2:c.*6924_*6943del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_015153.4:c.*6924_*6943del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001142800.2:c.9380_9399del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001292009.2:c.9443_9462del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001169039GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jan 15, 2019) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV001169039.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.9317_9336del20 variant in the EYS gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.9317_9336del20 variant causes a frameshift starting with codon Threonine 3106, changes this amino acid to a Lysine residue, and creates a premature Stop codon at position 13 of the new reading frame, denoted p.Thr3106LysfsX13. This variant is predicted to cause loss of normal protein function through protein truncation, as the last 39 amino acids are lost and replaced with 12 incorrect amino acids. The c.9317_9336del20 variant is observed in 2/14976 (0.013%) alleles from individuals of non-Finnish European background in large population cohorts (Lek et al., 2016). We interpret c.9317_9336del20 as a likely pathogenic variant.

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

Last Updated: Sep 1, 2024