NM_201253.3(CRB1):c.3106G>A (p.Glu1036Lys) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 18, 2022
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:: RCV002933082.3

Allele description [Variation Report for NM_201253.3(CRB1):c.3106G>A (p.Glu1036Lys)]

NM_201253.3(CRB1):c.3106G>A (p.Glu1036Lys)

Gene:

CRB1:crumbs cell polarity complex component 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q31.3

Genomic location:

Preferred name:

NM_201253.3(CRB1):c.3106G>A (p.Glu1036Lys)

HGVS:

NC_000001.11:g.197434969G>A
NG_008483.2:g.238508G>A
NG_008483.3:g.238467G>A
NM_001193640.2:c.2770G>A
NM_001257965.2:c.3034G>A
NM_001257966.2:c.2129-631G>A
NM_201253.3:c.3106G>AMANE SELECT
NP_001180569.1:p.Glu924Lys
NP_001244894.1:p.Glu1012Lys
NP_957705.1:p.Glu1036Lys
NC_000001.10:g.197404099G>A
NR_047563.2:n.3059G>A
NR_047564.2:n.3267G>A

Protein change:

E1012K

Molecular consequence:

NM_001257966.2:c.2129-631G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001193640.2:c.2770G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001257965.2:c.3034G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_201253.3:c.3106G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_047563.2:n.3059G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_047564.2:n.3267G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Retinitis pigmentosa 12 (RP12)
Synonyms:: RP 12; RP WITH OR WITHOUT PPRPE; RP WITH OR WITHOUT PRESERVED PARAARTERIOLE RETINAL PIGMENT EPITHELIUM; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010818; MedGen: C1838647; Orphanet: 791; OMIM: 600105

Name:: Leber congenital amaurosis 8 (LCA8)
Identifiers:: MONDO: MONDO:0013453; MedGen: C3151202; Orphanet: 65; OMIM: 613835

Recent activity

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PREDICTED: similar to sphingosine 1-phosphate phosphohydrolase 2 [Homo sapiens]
PREDICTED: similar to sphingosine 1-phosphate phosphohydrolase 2 [Homo sapiens]
gi|113414274|ref|XP_001128702.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003262943	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 18, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003262943

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 18, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV003262943.2

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

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CRB1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with CRB1-related conditions. This variant is present in population databases (rs563857130, gnomAD 0.006%). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1036 of the CRB1 protein (p.Glu1036Lys).

#	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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