NM_000512.5(GALNS):c.1012C>T (p.Gln338Ter) AND Mucopolysaccharidosis, MPS-IV-A

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Nov 7, 2021
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:: RCV001358675.7

Allele description [Variation Report for NM_000512.5(GALNS):c.1012C>T (p.Gln338Ter)]

NM_000512.5(GALNS):c.1012C>T (p.Gln338Ter)

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.1012C>T (p.Gln338Ter)

HGVS:

NC_000016.10:g.88826829G>A
NG_008667.1:g.35138C>T
NM_000512.5:c.1012C>TMANE SELECT
NM_001323543.2:c.457C>T
NM_001323544.2:c.1030C>T
NP_000503.1:p.Gln338Ter
NP_001310472.1:p.Gln153Ter
NP_001310473.1:p.Gln344Ter
NC_000016.9:g.88893237G>A

Protein change:

Q153*

Links:

dbSNP: rs767131589

NCBI 1000 Genomes Browser:

rs767131589

Molecular consequence:

NM_000512.5:c.1012C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001323543.2:c.457C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001323544.2:c.1030C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Mucopolysaccharidosis, MPS-IV-A (MPS4A)
Synonyms:: MPS IVA; Morquio syndrome A; MPS 4A; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009659; MedGen: C0086651; Orphanet: 309297; Orphanet: 582; OMIM: 253000

Recent activity

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Homo sapiens leukocyte specific transcript 1 (LST1), transcript variant 5, mRNA
Homo sapiens leukocyte specific transcript 1 (LST1), transcript variant 5, mRNA
gi|45580735|ref|NM_205840.1|

Nucleotide
Homo sapiens leukocyte specific transcript 1 (LST1), mRNA
Homo sapiens leukocyte specific transcript 1 (LST1), mRNA
gi|6005740|ref|NM_007161.1|

Nucleotide
U exon, partial [Human adenovirus 2]
U exon, partial [Human adenovirus 2]
gi|56160508|ref|AP_000189.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001547875	Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 1, 2021)	germline	curation	PubMed (4) [See all records that cite these PMIDs] 15235041, 9298823, 34387910, 25741868
SCV001554472	Centre for Inherited Metabolic Diseases, Karolinska University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 7, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002045003	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 7, 2021)	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

SCV001547875

Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 1, 2021)

germline

curation

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

SCV001554472

Centre for Inherited Metabolic Diseases, Karolinska University Hospital

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 7, 2021)

germline

clinical testing

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

SCV002045003

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 7, 2021)

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	yes	1	not provided	not provided	1	not provided	curation, clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mucopolysaccharidosis IVA: identification of mutations and methylation study in GALNS gene.

Tomatsu S, Nishioka T, Montaño AM, Gutierrez MA, Pena OS, Orii KO, Sly WS, Yamaguchi S, Orii T, Paschke E, Kircher SG, Noguchi A.

J Med Genet. 2004 Jul;41(7):e98. No abstract available.

PubMed [citation]

PMID:: 15235041
PMCID:: PMC1735846

Identification of 31 novel mutations in the N-acetylgalactosamine-6-sulfatase gene reveals excessive allelic heterogeneity among patients with Morquio A syndrome.

Bunge S, Kleijer WJ, Tylki-Szymanska A, Steglich C, Beck M, Tomatsu S, Fukuda S, Poorthuis BJ, Czartoryska B, Orii T, Gal A.

Hum Mutat. 1997;10(3):223-32.

PubMed [citation]

PMID:: 9298823

See all PubMed Citations (4)

Details of each submission

From Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova, SCV001547875.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (4)

Description

Nonsense variant (PVS1_very strong); the prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_moderate); very low frequency in gnomAD v2.1.1 (PM2_moderate)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Centre for Inherited Metabolic Diseases, Karolinska University Hospital, SCV001554472.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	no	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	discovery		1	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002045003.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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