NM_003896.4(ST3GAL5):c.44A>G (p.Gln15Arg) AND GM3 synthase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 25, 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:: RCV001309897.8

Allele description [Variation Report for NM_003896.4(ST3GAL5):c.44A>G (p.Gln15Arg)]

NM_003896.4(ST3GAL5):c.44A>G (p.Gln15Arg)

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.44A>G (p.Gln15Arg)

HGVS:

NC_000002.12:g.85888862T>C
NG_012807.1:g.5173A>G
NM_001354223.2:c.-919A>G
NM_001354224.2:c.-581A>G
NM_001354226.2:c.-518A>G
NM_001354227.2:c.-228A>G
NM_001354229.2:c.-172A>G
NM_001354233.2:c.-958A>G
NM_001363847.1:c.44A>G
NM_003896.4:c.44A>GMANE SELECT
NP_001350776.1:p.Gln15Arg
NP_003887.3:p.Gln15Arg
NC_000002.11:g.86115985T>C

Protein change:

Q15R

Links:

dbSNP: rs1280213817

NCBI 1000 Genomes Browser:

rs1280213817

Molecular consequence:

NM_001354223.2:c.-919A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354224.2:c.-581A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354226.2:c.-518A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354227.2:c.-228A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354229.2:c.-172A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354233.2:c.-958A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001363847.1:c.44A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003896.4:c.44A>G - 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
SCV001499411	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 25, 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

SCV001499411

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 25, 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, SCV001499411.4

#	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 glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 15 of the ST3GAL5 protein (p.Gln15Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ST3GAL5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1012008). 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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