NM_000554.6(CRX):c.76_80del (p.Met26fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 21, 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:: RCV001365217.5

Allele description [Variation Report for NM_000554.6(CRX):c.76_80del (p.Met26fs)]

NM_000554.6(CRX):c.76_80del (p.Met26fs)

Gene:

CRX:cone-rod homeobox [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_000554.6(CRX):c.76_80del (p.Met26fs)

HGVS:

NC_000019.10:g.47834519_47834523del
NG_008605.1:g.17678_17682del
NM_000554.6:c.76_80delMANE SELECT
NP_000545.1:p.Met26fs
NC_000019.9:g.48337776_48337780del

Protein change:

M26fs

Links:

dbSNP: rs2123738324

NCBI 1000 Genomes Browser:

rs2123738324

Molecular consequence:

NM_000554.6:c.76_80del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Leber congenital amaurosis 7 (LCA7)
Identifiers:: MONDO: MONDO:0013449; MedGen: C3151192; Orphanet: 65; OMIM: 613829

Name:: Cone-rod dystrophy 2 (CORD2)
Synonyms:: CONE-ROD RETINAL DYSTROPHY; Cone-rod retinal dystrophy 2
Identifiers:: MONDO: MONDO:0007362; MedGen: C3489532; Orphanet: 1872; OMIM: 120970

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001561480	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 21, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 27208204, 31626798, 35934205, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001561480

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 21, 2023)

germline

clinical testing

PubMed (4)
[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

Molecular findings from 537 individuals with inherited retinal disease.

Ellingford JM, Barton S, Bhaskar S, O'Sullivan J, Williams SG, Lamb JA, Panda B, Sergouniotis PI, Gillespie RL, Daiger SP, Hall G, Gale T, Lloyd IC, Bishop PN, Ramsden SC, Black GCM.

J Med Genet. 2016 Nov;53(11):761-767. doi: 10.1136/jmedgenet-2016-103837. Epub 2016 May 11.

PubMed [citation]

PMID:: 27208204
PMCID:: PMC5106339

Pathogenicity discrimination and genetic test reference for CRX variants based on genotype-phenotype analysis.

Yi Z, Xiao X, Li S, Sun W, Zhang Q.

Exp Eye Res. 2019 Dec;189:107846. doi: 10.1016/j.exer.2019.107846. Epub 2019 Oct 15.

PubMed [citation]

PMID:: 31626798

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001561480.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant has not been reported in the literature in individuals affected with CRX-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Met26Profs*43) in the CRX gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CRX are known to be pathogenic (PMID: 27208204, 31626798, 35934205). ClinVar contains an entry for this variant (Variation ID: 1056395). 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: Mar 5, 2024

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