NM_194318.4(B3GLCT):c.1487A>G (p.Glu496Gly) AND Peters plus syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 6, 2020
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:: RCV001370570.7

Allele description [Variation Report for NM_194318.4(B3GLCT):c.1487A>G (p.Glu496Gly)]

NM_194318.4(B3GLCT):c.1487A>G (p.Glu496Gly)

Gene:

B3GLCT:beta 3-glucosyltransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q12.3

Genomic location:

Preferred name:

NM_194318.4(B3GLCT):c.1487A>G (p.Glu496Gly)

HGVS:

NC_000013.11:g.31329658A>G
NG_011732.2:g.134684A>G
NM_194318.4:c.1487A>GMANE SELECT
NP_919299.3:p.Glu496Gly
NC_000013.10:g.31903795A>G

Protein change:

E496G

Links:

dbSNP: rs1875814798

NCBI 1000 Genomes Browser:

rs1875814798

Molecular consequence:

NM_194318.4:c.1487A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Peters plus syndrome
Synonyms:: Peters anomaly with short limb dwarfism; Krause-Kivlin syndrome
Identifiers:: MONDO: MONDO:0009856; MedGen: C0796012; Orphanet: 709; OMIM: 261540

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Chain L, Cytochrome c oxidase subunit 7C, mitochondrial
Chain L, Cytochrome c oxidase subunit 7C, mitochondrial
gi|2069592686|pdb|7EV7|L

Protein
(("clinical guidelines"[Resource Type]) OR "practice guideline"[P... (6)
(("clinical guidelines"[Resource Type]) OR "practice guideline"[Publication Type]) AND ("Rectum mucinous adenocarcinoma")
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Component(Core) Links for Nucleotide (Select 432118651) (2)
Nucleotide
Concise Conserved Domain Links for Protein (Select 1034606252) (2)
Conserved Domains
DFR85_RS21490 [Acidianus brierleyi]
DFR85_RS21490 [Acidianus brierleyi]
Gene ID:36831617

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001567089	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 6, 2020)	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

SCV001567089

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 6, 2020)

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, SCV001567089.4

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

Description

This variant has not been reported in the literature in individuals with B3GLCT-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with glycine at codon 496 of the B3GLCT protein (p.Glu496Gly). The glutamic acid residue is moderately conserved and there is a moderate physicochemical difference between glutamic acid and glycine.

#	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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