Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_001122769.3(LCA5):c.835C>T (p.Gln279Ter)

Help
Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Mar 28, 2019)
Last evaluated:
Dec 13, 2018
Accession:
VCV000000968.3
Variation ID:
968
Description:
single nucleotide variant
Help

NM_001122769.3(LCA5):c.835C>T (p.Gln279Ter)

Allele ID
16007
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q14.1
Genomic location
6: 79493636 (GRCh38) GRCh38 UCSC
6: 80203353 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.80203353G>A
NC_000006.12:g.79493636G>A
NM_001122769.3:c.835C>T NP_001116241.1:p.Gln279Ter nonsense
... more HGVS
Protein change
Q279*
Other names
-
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00012
Exome Aggregation Consortium (ExAC) 0.00012
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Links
ClinGen: CA204615
OMIM: 611408.0003
dbSNP: rs121918165
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, single submitter Apr 27, 2017 RCV000001019.4
Pathogenic 1 criteria provided, single submitter Sep 10, 2013 RCV000190663.2
Pathogenic 1 criteria provided, single submitter Dec 13, 2018 RCV000812173.1
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
LCA5 - - GRCh38
GRCh37
75 91

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 10, 2013)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV000244103.4
Submitted: (Nov 14, 2017)
Evidence details
Publications
PubMed (3)
Pathogenic
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Leber congenital amaurosis 5
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000465592.3
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (5)
Comment:
The LCA5 c.835C>T (p.Gln279Ter) variant is a stop-gained variant that is described in four studies, in which it was found in a homozygous state in ... (more)
Pathogenic
(Dec 13, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV000952477.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change creates a premature translational stop signal (p.Gln279*) in the LCA5 gene. It is expected to result in an absent or disrupted protein ... (more)
pathologic
(May 02, 2013)
no assertion criteria provided
Method: curation
Leber Congenital Amaurosis
Allele origin: not provided
GeneReviews
Accession: SCV000087066.1
Submitted: (Apr 30, 2013)
Evidence details
Comment:
Converted during submission to Pathogenic.
Pathogenic
(Jul 01, 2007)
no assertion criteria provided
Method: literature only
LEBER CONGENITAL AMAUROSIS 5
Allele origin: germline
OMIM
Accession: SCV000021169.2
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Citations for this variant

Title Author Journal Year Link
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Farwell KD Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25356970
Screening of a large cohort of leber congenital amaurosis and retinitis pigmentosa patients identifies novel LCA5 mutations and new genotype-phenotype correlations. Mackay DS Human mutation 2013 PMID: 23946133
Leber Congenital Amaurosis Weleber RG - 2013 PMID: 20301475
Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice. Boldt K The Journal of clinical investigation 2011 PMID: 21606596
Leber congenital amaurosis caused by Lebercilin (LCA5) mutation: retained photoreceptors adjacent to retinal disorganization. Jacobson SG Molecular vision 2009 PMID: 19503738
Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. den Hollander AI Nature genetics 2007 PMID: 17546029

Record last updated Oct 27, 2019