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NM_145200.5(CABP4):c.292C>T (p.Arg98Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 18, 2024
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:
RCV002032536.4

Allele description [Variation Report for NM_145200.5(CABP4):c.292C>T (p.Arg98Ter)]

NM_145200.5(CABP4):c.292C>T (p.Arg98Ter)

Gene:
CABP4:calcium binding protein 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.2
Genomic location:
Preferred name:
NM_145200.5(CABP4):c.292C>T (p.Arg98Ter)
HGVS:
  • NC_000011.10:g.67455715C>T
  • NG_021211.1:g.5369C>T
  • NM_001300895.3:c.-92C>T
  • NM_001300896.3:c.-106C>T
  • NM_001379183.1:c.-106C>T
  • NM_145200.5:c.292C>TMANE SELECT
  • NP_660201.1:p.Arg98Ter
  • NC_000011.9:g.67223186C>T
  • NR_166529.1:n.362C>T
Protein change:
R98*
Links:
dbSNP: rs777555935
NCBI 1000 Genomes Browser:
rs777555935
Molecular consequence:
  • NM_001300895.3:c.-92C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001300896.3:c.-106C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001379183.1:c.-106C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_166529.1:n.362C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_145200.5:c.292C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV002232539Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 18, 2024) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Congenital stationary night blindness: an analysis and update of genotype-phenotype correlations and pathogenic mechanisms.

Zeitz C, Robson AG, Audo I.

Prog Retin Eye Res. 2015 Mar;45:58-110. doi: 10.1016/j.preteyeres.2014.09.001. Epub 2014 Oct 13. Review.

PubMed [citation]
PMID:
25307992

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002232539.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Arg98*) in the CABP4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CABP4 are known to be pathogenic (PMID: 25307992). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CABP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 1184508). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024