NM_000554.6(CRX):c.116_127del (p.Gln39_Glu42del) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 25, 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:: RCV002839076.2

Allele description [Variation Report for NM_000554.6(CRX):c.116_127del (p.Gln39_Glu42del)]

NM_000554.6(CRX):c.116_127del (p.Gln39_Glu42del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_000554.6(CRX):c.116_127del (p.Gln39_Glu42del)

HGVS:

NC_000019.10:g.47836258_47836269del
NG_008605.1:g.19417_19428del
NM_000554.6:c.116_127delMANE SELECT
NP_000545.1:p.Gln39_Glu42del
NC_000019.9:g.48339512_48339523del
NC_000019.9:g.48339515_48339526del

Molecular consequence:

NM_000554.6:c.116_127del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV003219158	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 25, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 26161267, 29785639, 31626798, 32533067, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003219158

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 25, 2023)

germline

clinical testing

PubMed (5)
[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

Retinitis Pigmentosa with EYS Mutations Is the Most Prevalent Inherited Retinal Dystrophy in Japanese Populations.

Arai Y, Maeda A, Hirami Y, Ishigami C, Kosugi S, Mandai M, Kurimoto Y, Takahashi M.

J Ophthalmol. 2015;2015:819760. doi: 10.1155/2015/819760. Epub 2015 Jun 16.

PubMed [citation]

PMID:: 26161267
PMCID:: PMC4487330

Development of a molecular diagnostic test for Retinitis Pigmentosa in the Japanese population.

Maeda A, Yoshida A, Kawai K, Arai Y, Akiba R, Inaba A, Takagi S, Fujiki R, Hirami Y, Kurimoto Y, Ohara O, Takahashi M.

Jpn J Ophthalmol. 2018 Jul;62(4):451-457. doi: 10.1007/s10384-018-0601-x. Epub 2018 May 21.

PubMed [citation]

PMID:: 29785639

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003219158.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant has not been reported in the literature in individuals affected with CRX-related conditions. ClinVar contains an entry for this variant (Variation ID: 2014678). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant disrupts a region of the CRX protein in which other variant(s) (p.Arg40Trp) have been determined to be pathogenic (PMID: 26161267, 29785639, 31626798, 32533067). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This variant, c.116_127del, results in the deletion of 4 amino acid(s) of the CRX protein (p.Gln39_Glu42del), but otherwise preserves the integrity of the reading frame.

#	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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