NM_003896.4(ST3GAL5):c.580C>T (p.Arg194Cys) AND GM3 synthase deficiency

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 22, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001142220.6

Allele description [Variation Report for NM_003896.4(ST3GAL5):c.580C>T (p.Arg194Cys)]

NM_003896.4(ST3GAL5):c.580C>T (p.Arg194Cys)

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.580C>T (p.Arg194Cys)

HGVS:

NC_000002.12:g.85847943G>A
NG_012807.1:g.46092C>T
NM_001042437.2:c.511C>T
NM_001354223.2:c.196C>T
NM_001354224.2:c.196C>T
NM_001354226.2:c.196C>T
NM_001354227.2:c.496C>T
NM_001354229.2:c.496C>T
NM_001354233.2:c.196C>T
NM_001354234.1:c.196C>T
NM_001354238.1:c.496C>T
NM_001354247.1:c.-325C>T
NM_001354248.1:c.196C>T
NM_001363847.1:c.580C>T
NM_003896.4:c.580C>TMANE SELECT
NP_001035902.1:p.Arg171Cys
NP_001341152.1:p.Arg66Cys
NP_001341153.1:p.Arg66Cys
NP_001341155.1:p.Arg66Cys
NP_001341156.1:p.Arg166Cys
NP_001341158.1:p.Arg166Cys
NP_001341162.1:p.Arg66Cys
NP_001341163.1:p.Arg66Cys
NP_001341167.1:p.Arg166Cys
NP_001341177.1:p.Arg66Cys
NP_001350776.1:p.Arg194Cys
NP_003887.3:p.Arg194Cys
NC_000002.11:g.86075066G>A
NC_000002.11:g.86075066G>A
NM_003896.3:c.580C>T

Protein change:

R166C

Links:

dbSNP: rs377626779

NCBI 1000 Genomes Browser:

rs377626779

Molecular consequence:

NM_001354247.1:c.-325C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001042437.2:c.511C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354223.2:c.196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354224.2:c.196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354226.2:c.196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354227.2:c.496C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354229.2:c.496C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354233.2:c.196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354234.1:c.196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354238.1:c.496C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354248.1:c.196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363847.1:c.580C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003896.4:c.580C>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
SCV001302639	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Jan 12, 2018)	germline	clinical testing	Citation Link,
SCV003244431	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 22, 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

SCV001302639

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Jan 12, 2018)

germline

clinical testing

Citation Link,

SCV003244431

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 22, 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 Illumina Laboratory Services, Illumina, SCV001302639.1

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003244431.1

#	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 arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 194 of the ST3GAL5 protein (p.Arg194Cys). This variant is present in population databases (rs377626779, gnomAD 0.03%). 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: 898381). 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 disruptive. 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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