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NM_000512.5(GALNS):c.239C>T (p.Ser80Leu) AND GALNS-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 7, 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:
RCV003420080.4

Allele description [Variation Report for NM_000512.5(GALNS):c.239C>T (p.Ser80Leu)]

NM_000512.5(GALNS):c.239C>T (p.Ser80Leu)

Gene:
GALNS:galactosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000512.5(GALNS):c.239C>T (p.Ser80Leu)
HGVS:
  • NC_000016.10:g.88842711G>A
  • NG_008667.1:g.19256C>T
  • NM_000512.5:c.239C>TMANE SELECT
  • NM_001323543.2:c.-311-740C>T
  • NM_001323544.2:c.257C>T
  • NP_000503.1:p.Ser80Leu
  • NP_001310473.1:p.Ser86Leu
  • NC_000016.9:g.88909119G>A
  • NM_000512.4:c.239C>T
Protein change:
S80L
Links:
dbSNP: rs1209154325
NCBI 1000 Genomes Browser:
rs1209154325
Molecular consequence:
  • NM_001323543.2:c.-311-740C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000512.5:c.239C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323544.2:c.257C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
GALNS-related disorder
Synonyms:
GALNS-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004108330PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jun 7, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004108330.1

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

Description

The GALNS c.239C>T variant is predicted to result in the amino acid substitution p.Ser80Leu. This variant was reported in homozygous and compound heterozygous state in multiple individuals with Mucopolysaccharidosis IVA (Tomatsu et al. 1997. PubMed ID: 9375852; Pachajoa et al. 2021. PubMed ID: 34542925; Pollard et al. 2012. PubMed ID: 22976768; Tapiero-Rodriguez et al. 2018. PubMed ID: 29731656). In vitro and in vivo studies show that this variant results in significantly reduced enzymatic activity (Tomatsu et al. 1997. PubMed ID: 9375852; Tapiero-Rodriguez et al. 2018. PubMed ID: 29731656). This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-88909119-G-A). This variant is interpreted as likely pathogenic.

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

Last Updated: Apr 13, 2025