NM_145200.5(CABP4):c.233_234del (p.Glu78fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 26, 2017
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:: RCV002890623.2

Allele description [Variation Report for NM_145200.5(CABP4):c.233_234del (p.Glu78fs)]

NM_145200.5(CABP4):c.233_234del (p.Glu78fs)

Gene:

CABP4:calcium binding protein 4 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q13.2

Genomic location:

Preferred name:

NM_145200.5(CABP4):c.233_234del (p.Glu78fs)

HGVS:

NC_000011.10:g.67455654AG[1]
NG_021211.1:g.5308AG[1]
NM_001300895.3:c.-153AG[1]
NM_001300896.3:c.-112-53_-112-52del
NM_001379183.1:c.-167AG[1]
NM_145200.5:c.233_234delMANE SELECT
NP_660201.1:p.Glu78fs
NC_000011.9:g.67223124_67223125del
NC_000011.9:g.67223125AG[1]
NR_166529.1:n.301AG[1]

Protein change:

E78fs

Molecular consequence:

NM_001300895.3:c.-153AG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001379183.1:c.-167AG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_145200.5:c.233_234del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001300896.3:c.-112-53_-112-52del - intron variant - [Sequence Ontology: SO:0001627]
NR_166529.1:n.301AG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003244277	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 26, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25307992, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003244277

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 26, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV003244277.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change deletes 2 nucleotide from exon 1 of the CABP4 mRNA (c.233_234delAG), causing a frameshift at codon 78. This creates a premature translational stop signal (p.Glu78Glyfs*24) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, loss-of-function variants in CABP4 are known to be pathogenic (PMID: 25307992). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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