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NM_001367624.2(ZNF469):c.5402del (p.Val1801fs) AND Brittle cornea syndrome 1

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 24, 2023
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:
RCV003123419.3

Allele description [Variation Report for NM_001367624.2(ZNF469):c.5402del (p.Val1801fs)]

NM_001367624.2(ZNF469):c.5402del (p.Val1801fs)

Gene:
ZNF469:zinc finger protein 469 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.2
Genomic location:
Preferred name:
NM_001367624.2(ZNF469):c.5402del (p.Val1801fs)
HGVS:
  • NC_000016.10:g.88432872del
  • NG_012236.2:g.10402del
  • NM_001367624.2:c.5402delMANE SELECT
  • NP_001354553.1:p.Val1801Alafs
  • NP_001354553.1:p.Val1801fs
  • NC_000016.9:g.88499280del
  • NM_001367624.1:c.5402delT
  • NM_001367624.2:c.5402delTMANE SELECT
Protein change:
V1801fs
Molecular consequence:
  • NM_001367624.2:c.5402del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Brittle cornea syndrome 1 (BCS1)
Synonyms:
EDS6B; EDS VIB (formerly); Ehlers-Danlos syndrome type 6B (formerly); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0024543; MedGen: C0268344; Orphanet: 90354; OMIM: 229200

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003800882Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Jan 24, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003800882.2

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

Description

Variant summary: ZNF469 c.5402delT (p.Val1801AlafsX65) results in a premature termination codon located at the 3' terminus, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant disrupts >2000 amino acids of the protein. Truncations downstream of this position have been reported in association with Brittle cornea syndrome in HGMD and classified as pathogenic in ClinVar. The variant was absent in 152922 control chromosomes. To our knowledge, no occurrence of c.5402delT in individuals affected with Brittle Cornea Syndrome 1 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Nov 11, 2023