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NM_018418.5(SPATA7):c.1293dup (p.Asp432Ter) AND Leber congenital amaurosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 13, 2022
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:
RCV002266502.1

Allele description [Variation Report for NM_018418.5(SPATA7):c.1293dup (p.Asp432Ter)]

NM_018418.5(SPATA7):c.1293dup (p.Asp432Ter)

Gene:
SPATA7:spermatogenesis associated 7 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
14q31.3
Genomic location:
Preferred name:
NM_018418.5(SPATA7):c.1293dup (p.Asp432Ter)
HGVS:
  • NC_000014.9:g.88437915dup
  • NG_021183.1:g.57272dup
  • NM_001040428.4:c.1197dup
  • NM_018418.5:c.1293dupMANE SELECT
  • NP_001035518.1:p.Asp400Ter
  • NP_060888.2:p.Asp432Ter
  • NC_000014.8:g.88904259dup
  • NM_018418.4:c.1293dupT
Protein change:
D400*
Links:
dbSNP: rs2077134911
NCBI 1000 Genomes Browser:
rs2077134911
Molecular consequence:
  • NM_001040428.4:c.1197dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_018418.5:c.1293dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Leber congenital amaurosis (LCA)
Synonyms:
Congenital retinal blindness; Leber's amaurosis
Identifiers:
MONDO: MONDO:0018998; MeSH: D057130; MedGen: C0339527; OMIM: PS204000

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002547510Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(May 13, 2022) 		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, SCV002547510.1

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

Description

Variant summary: SPATA7 c.1293dupT (p.Asp432X) located in the last exon results in a premature termination codon, 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. Truncations downstream of this position have not been observed at our laboratory but have been reported in association with Leber Congenital Amaurosis and related phenotypes in the HGMD database. The variant was absent in 250522 control chromosomes. To our knowledge, no occurrence of c.1293dupT in individuals affected with Leber Congenital Amaurosis 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: Dec 24, 2023