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NM_000512.5(GALNS):c.[1140-730_1365-1530del;121-2779_567-248del] AND Mucopolysaccharidosis, MPS-IV-A

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 1, 2021
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:
RCV001578480.4

Alleles description [Variation Report for NM_000512.5(GALNS):c.[1140-730_1365-1530del;121-2779_567-248del]]

NM_000512.5(GALNS):c.1140-730_1365-1530del

Gene:
GALNS:galactosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000512.5(GALNS):c.1140-730_1365-1530del
HGVS:
  • NC_000016.10:g.88819654_88825599del
  • NG_008667.1:g.36368_42313del
  • NM_000512.5:c.1140-730_1365-1530delMANE SELECT
  • NM_001323543.2:c.585-730_810-1530del
  • NM_001323544.2:c.1158-730_1383-1530del
  • NC_000016.9:g.88886062_88892007del
Molecular consequence:
  • NM_000512.5:c.1140-730_1365-1530del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001323543.2:c.585-730_810-1530del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001323544.2:c.1158-730_1383-1530del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000512.5:c.1140-730_1365-1530del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001323543.2:c.585-730_810-1530del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001323544.2:c.1158-730_1383-1530del - splice donor variant - [Sequence Ontology: SO:0001575]

NM_000512.5(GALNS):c.121-2779_567-248del

Gene:
GALNS:galactosamine (N-acetyl)-6-sulfatase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q24.3
Genomic location:
Preferred name:
NM_000512.5(GALNS):c.121-2779_567-248del
HGVS:
  • NC_000016.10:g.88836515_88845608del
  • NG_008667.1:g.16359_25452del
  • NM_000512.5:c.121-2779_567-248delMANE SELECT
  • NM_001323543.2:c.-311-3637_12-248del
  • NM_001323544.2:c.-32-2409_585-248del
  • NC_000016.9:g.88902923_88912016del
Molecular consequence:
  • NM_001323543.2:c.-311-3637_12-248del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001323544.2:c.-32-2409_585-248del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_000512.5:c.121-2779_567-248del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001323543.2:c.-311-3637_12-248del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001323544.2:c.-32-2409_585-248del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000512.5:c.121-2779_567-248del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001323543.2:c.-311-3637_12-248del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001323544.2:c.-32-2409_585-248del - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV001547595Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Feb 1, 2021) 		germlinecuration

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Mucopolysaccharidosis IVA: screening and identification of mutations of the N-acetylgalactosamine-6-sulfate sulfatase gene.

Ogawa T, Tomatsu S, Fukuda S, Yamagishi A, Rezvi GM, Sukegawa K, Kondo N, Suzuki Y, Shimozawa N, Orü T.

Hum Mol Genet. 1995 Mar;4(3):341-9.

PubMed [citation]
PMID:
7795586

Mucopolysaccharidosis IVA: four new exonic mutations in patients with N-acetylgalactosamine-6-sulfate sulfatase deficiency.

Tomatsu S, Fukuda S, Yamagishi A, Cooper A, Wraith JF, Hori T, Kato Z, Yamada N, Isogai K, Sukegawa K, Kondo N, Suzuki Y, Shimozawa N, Orii T.

Am J Hum Genet. 1996 May;58(5):950-62.

PubMed [citation]
PMID:
8651279
PMCID:
PMC1914620
See all PubMed Citations (4)

Details of each submission

From Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV001547595.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (4)

Description

Multi-exon deletion (PVS1_very strong); in vivo functional studies supportive of a damaging effect on the gene product (low to null enzymatic activity in homozygotes; PS3_supporting); the prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_supporting); located in a mutational hot spot and/or critical and well-established functional domain without benign variation (PM1_moderate); absent from gnomAD v2.1.1 (PM2_moderate)

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

Last Updated: Apr 12, 2026

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