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NM_003896.4(ST3GAL5):c.64del (p.Ala22fs) AND GM3 synthase deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 18, 2023
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:
RCV003613633.2

Allele description [Variation Report for NM_003896.4(ST3GAL5):c.64del (p.Ala22fs)]

NM_003896.4(ST3GAL5):c.64del (p.Ala22fs)

Genes:
LOC129934236:ATAC-STARR-seq lymphoblastoid silent region 11709 [Gene]
ST3GAL5:ST3 beta-galactoside alpha-2,3-sialyltransferase 5 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p11.2
Genomic location:
Preferred name:
NM_003896.4(ST3GAL5):c.64del (p.Ala22fs)
HGVS:
  • NC_000002.12:g.85888843del
  • NG_012807.1:g.5193del
  • NG_012807.2:g.5192del
  • NG_167257.1:g.172del
  • NM_001354223.2:c.-899del
  • NM_001354224.2:c.-561del
  • NM_001354226.2:c.-498del
  • NM_001354227.2:c.-208del
  • NM_001354229.2:c.-152del
  • NM_001354233.2:c.-938del
  • NM_001363847.1:c.64del
  • NM_003896.4:c.64delMANE SELECT
  • NP_001350776.1:p.Ala22fs
  • NP_003887.3:p.Ala22fs
  • NC_000002.11:g.86115965del
  • NC_000002.11:g.86115966del
Protein change:
A22fs
Molecular consequence:
  • NM_001354223.2:c.-899del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354224.2:c.-561del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354226.2:c.-498del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354227.2:c.-208del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354229.2:c.-152del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354233.2:c.-938del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363847.1:c.64del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_003896.4:c.64del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004413947Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Aug 18, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Infantile-onset symptomatic epilepsy syndrome caused by a homozygous loss-of-function mutation of GM3 synthase.

Simpson MA, Cross H, Proukakis C, Priestman DA, Neville DC, Reinkensmeier G, Wang H, Wiznitzer M, Gurtz K, Verganelaki A, Pryde A, Patton MA, Dwek RA, Butters TD, Platt FM, Crosby AH.

Nat Genet. 2004 Nov;36(11):1225-9. Epub 2004 Oct 24.

PubMed [citation]
PMID:
15502825

Refractory epilepsy and mitochondrial dysfunction due to GM3 synthase deficiency.

Fragaki K, Ait-El-Mkadem S, Chaussenot A, Gire C, Mengual R, Bonesso L, Bénéteau M, Ricci JE, Desquiret-Dumas V, Procaccio V, Rötig A, Paquis-Flucklinger V.

Eur J Hum Genet. 2013 May;21(5):528-34. doi: 10.1038/ejhg.2012.202. Epub 2012 Sep 19.

PubMed [citation]
PMID:
22990144
PMCID:
PMC3641379
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004413947.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Ala22Argfs*15) in the ST3GAL5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ST3GAL5 are known to be pathogenic (PMID: 15502825, 22990144, 27232954). 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. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024