NM_003896.4(ST3GAL5):c.20G>T (p.Gly7Val) AND GM3 synthase deficiency

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:: RCV003085925.3

Allele description [Variation Report for NM_003896.4(ST3GAL5):c.20G>T (p.Gly7Val)]

NM_003896.4(ST3GAL5):c.20G>T (p.Gly7Val)

Genes:

LOC129934236:ATAC-STARR-seq lymphoblastoid silent region 11709 [Gene]
ST3GAL5:ST3 beta-galactoside alpha-2,3-sialyltransferase 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p11.2

Genomic location:

Preferred name:

NM_003896.4(ST3GAL5):c.20G>T (p.Gly7Val)

HGVS:

NC_000002.12:g.85888886C>A
NG_012807.2:g.5148G>T
NM_001354223.2:c.-943G>T
NM_001354224.2:c.-605G>T
NM_001354226.2:c.-542G>T
NM_001354227.2:c.-252G>T
NM_001354229.2:c.-196G>T
NM_001354233.2:c.-982G>T
NM_001363847.1:c.20G>T
NM_003896.4:c.20G>TMANE SELECT
NP_001350776.1:p.Gly7Val
NP_003887.3:p.Gly7Val
NC_000002.11:g.86116009C>A
NG_012807.1:g.5149G>T

Protein change:

G7V

Molecular consequence:

NM_001354223.2:c.-943G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354224.2:c.-605G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354226.2:c.-542G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354227.2:c.-252G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354229.2:c.-196G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354233.2:c.-982G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001363847.1:c.20G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003896.4:c.20G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: GM3 synthase deficiency (SPDRS)
Synonyms:: SALT AND PEPPER MENTAL RETARDATION SYNDROME; Salt and pepper developmental regression syndrome; Salt and pepper syndrome
Identifiers:: MONDO: MONDO:0018274; MedGen: C1836824; Orphanet: 171714; OMIM: 609056

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003472430	Labcorp Genetics (formerly Invitae), Labcorp	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

SCV003472430

Labcorp Genetics (formerly Invitae), Labcorp

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003472430.2

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

Description

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 is not present in population databases (gnomAD no frequency). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with ST3GAL5-related conditions. This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 7 of the ST3GAL5 protein (p.Gly7Val).

#	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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