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NM_000512.5(GALNS):c.1483-2A>C AND Mucopolysaccharidosis, MPS-IV-A

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 13, 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:
RCV003222545.2

Allele description [Variation Report for NM_000512.5(GALNS):c.1483-2A>C]

NM_000512.5(GALNS):c.1483-2A>C

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.1483-2A>C
HGVS:
  • NC_000016.10:g.88814527T>G
  • NG_008013.1:g.2408A>C
  • NG_008667.1:g.47440A>C
  • NM_000512.5:c.1483-2A>CMANE SELECT
  • NM_001323543.2:c.928-2A>C
  • NM_001323544.2:c.1501-2A>C
  • NC_000016.9:g.88880935T>G
Links:
dbSNP: rs2142967340
NCBI 1000 Genomes Browser:
rs2142967340
Molecular consequence:
  • NM_000512.5:c.1483-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001323543.2:c.928-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001323544.2:c.1501-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
1

Condition(s)

Name:
Mucopolysaccharidosis, MPS-IV-A (MPS4A)
Synonyms:
MORQUIO SYNDROME A; GALACTOSAMINE-6-SULFATASE DEFICIENCY; GALNS DEFICIENCY; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009659; MedGen: C0086651; Orphanet: 309297; Orphanet: 582; OMIM: 253000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003915846Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Apr 13, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not 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 Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics, SCV003915846.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

A Heterozygous missense variation in intron 14 of the GALNS gene was detected. The observed variant c.1483-2A>C has not been reported in the 1000 genomes and gnomAD databases. The in silico prediction of the variant is disease causing by MutationTaster. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: May 16, 2025