NM_012200.4(B3GAT3):c.517G>A (p.Gly173Ser) AND Larsen-like syndrome, B3GAT3 type

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 30, 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:: RCV002994047.1

Allele description

NM_012200.4(B3GAT3):c.517G>A (p.Gly173Ser)

Gene:

B3GAT3:beta-1,3-glucuronyltransferase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q12.3

Genomic location:

Preferred name:

NM_012200.4(B3GAT3):c.517G>A (p.Gly173Ser)

HGVS:

NC_000011.10:g.62617088C>T
NG_009845.1:g.9348C>T
NG_009845.2:g.8833C>T
NG_031863.1:g.10088G>A
NG_122728.1:g.543C>T
NG_122729.1:g.42C>T
NM_001288721.2:c.496G>A
NM_001288722.2:c.517G>A
NM_001288723.2:c.517G>A
NM_012200.4:c.517G>AMANE SELECT
NP_001275650.1:p.Gly166Ser
NP_001275651.1:p.Gly173Ser
NP_001275652.1:p.Gly173Ser
NP_036332.2:p.Gly173Ser
NC_000011.9:g.62384560C>T
NR_109991.2:n.546G>A

Protein change:

G166S

Molecular consequence:

NM_001288721.2:c.496G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001288722.2:c.517G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001288723.2:c.517G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_012200.4:c.517G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_109991.2:n.546G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Larsen-like syndrome, B3GAT3 type
Synonyms:: LARSEN SYNDROME, AUTOSOMAL RECESSIVE; Multiple joint dislocations, short stature, craniofacial dysmorphism, and congenital heart defects; MULTIPLE JOINT DISLOCATIONS, SHORT STATURE, AND CRANIOFACIAL DYSMORPHISM WITH OR WITHOUT CONGENITAL HEART DEFECTS
Identifiers:: MONDO: MONDO:0009511; MedGen: C3278404; Orphanet: 284139; OMIM: 245600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003297889	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 30, 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

SCV003297889

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 30, 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 Invitae, SCV003297889.1

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 173 of the B3GAT3 protein (p.Gly173Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with B3GAT3-related conditions. 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. 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: Feb 13, 2023

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