NM_002900.3(RBP3):c.1553A>G (p.Gln518Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 15, 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:: RCV001053424.7

Allele description [Variation Report for NM_002900.3(RBP3):c.1553A>G (p.Gln518Arg)]

NM_002900.3(RBP3):c.1553A>G (p.Gln518Arg)

Gene:

RBP3:retinol binding protein 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q11.22

Genomic location:

Preferred name:

NM_002900.3(RBP3):c.1553A>G (p.Gln518Arg)

HGVS:

NC_000010.11:g.47350037A>G
NG_029718.1:g.6667A>G
NM_002900.3:c.1553A>GMANE SELECT
NP_002891.1:p.Gln518Arg
NC_000010.10:g.48389325T>C
NM_002900.2:c.1553A>G
P10745:p.Gln518Arg

Protein change:

Q518R

Links:

UniProtKB: P10745#VAR_069683; dbSNP: rs563600593

NCBI 1000 Genomes Browser:

rs563600593

Molecular consequence:

NM_002900.3:c.1553A>G - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001217683	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 15, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19074801, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001217683

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 15, 2022)

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

A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa.

den Hollander AI, McGee TL, Ziviello C, Banfi S, Dryja TP, Gonzalez-Fernandez F, Ghosh D, Berson EL.

Invest Ophthalmol Vis Sci. 2009 Apr;50(4):1864-72. doi: 10.1167/iovs.08-2497. Epub 2008 Dec 13.

PubMed [citation]

PMID:: 19074801
PMCID:: PMC2823395

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, SCV001217683.4

#	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 replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 518 of the RBP3 protein (p.Gln518Arg). 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 missense change has been observed in individual(s) with retinal degeneration (PMID: 19074801). ClinVar contains an entry for this variant (Variation ID: 208306). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.

#	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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