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NM_000512.5(GALNS):c.901G>T (p.Gly301Cys)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 15, 2021)
Last evaluated:
Sep 15, 2021
Accession:
VCV000000708.9
Variation ID:
708
Description:
single nucleotide variant
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NM_000512.5(GALNS):c.901G>T (p.Gly301Cys)

Allele ID
15747
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 88832099 (GRCh38) GRCh38 UCSC
16: 88898507 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
P34059:p.Gly301Cys
NC_000016.10:g.88832099C>A
NC_000016.9:g.88898507C>A
... more HGVS
Protein change
G301C, G116C, G307C
Other names
-
Canonical SPDI
NC_000016.10:88832098:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00011
Trans-Omics for Precision Medicine (TOPMed) 0.00011
1000 Genomes Project 0.00080
The Genome Aggregation Database (gnomAD), exomes 0.00004
The Genome Aggregation Database (gnomAD) 0.00006
Links
ClinGen: CA221063
UniProtKB: P34059#VAR_007216
OMIM: 612222.0010
dbSNP: rs118204443
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 criteria provided, multiple submitters, no conflicts Feb 1, 2021 RCV000000743.13
Pathogenic 2 criteria provided, multiple submitters, no conflicts Sep 15, 2021 RCV000790840.2
Pathogenic 1 criteria provided, single submitter Apr 24, 2018 RCV000781400.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GALNS - - GRCh38
GRCh37
670 812

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Apr 24, 2018)
criteria provided, single submitter
Method: clinical testing
Morquio syndrome
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000919397.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: GALNS c.901G>T (p.Gly301Cys) results in a non-conservative amino acid change located in the sulfatase, N-terminal domain (IPR000917) of the encoded protein sequence. Five … (more)
Pathogenic
(Apr 20, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000232973.5
Submitted: (Jun 30, 2017)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Feb 01, 2021)
criteria provided, single submitter
Method: research
Mucopolysaccharidosis, MPS-IV-A
Allele origin: germline
Laboratory of Diagnosis and Therapy of Lysosomal Disorders,University of Padova
Accession: SCV001547832.2
Submitted: (Feb 22, 2021)
Evidence details
Publications
PubMed (12)
https://doi.org/10.1016/j.mgene.201  (more...)
Comment:
In vitro and in vivo functional studies supportive of a damaging effect on the gene product (low to null enzymatic activity in homozygotes; low to … (more)
Pathogenic
(Sep 15, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
(Autosomal recessive inheritance)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001905585.1
Submitted: (Sep 15, 2021)
Evidence details
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-IV-A
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000894088.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Mar 11, 2020)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-IV-A
Allele origin: germline
Invitae
Accession: SCV000825222.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (7)
Comment:
This sequence change replaces glycine with cysteine at codon 301 of the GALNS protein (p.Gly301Cys). The glycine residue is highly conserved and there is a … (more)
Pathogenic
(Nov 01, 1997)
no assertion criteria provided
Method: literature only
MUCOPOLYSACCHARIDOSIS, TYPE IVA
Allele origin: germline
OMIM
Accession: SCV000020893.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Molecular basis of mucopolysaccharidosis IVA (Morquio A syndrome): A review and classification of GALNS gene variants and reporting of 68 novel variants. Zanetti A Human mutation 2021 PMID: 34387910
Clinical characteristics of patients from Quebec, Canada, with Morquio A syndrome: a longitudinal observational study. Moisan L Orphanet journal of rare diseases 2020 PMID: 32993725
Clinical and molecular characteristics of colombian patients with mucopolysaccharidosis IVA, and description of a new galns gene mutation. Moreno Giraldo LJ Molecular genetics and metabolism reports 2018 PMID: 30094185
Elosulfase alfa for mucopolysaccharidosis type IVA: Real-world experience in 7 patients from the Spanish Morquio-A early access program. Pintos-Morell G Molecular genetics and metabolism reports 2018 PMID: 30023300
Determination of genotypic and clinical characteristics of Colombian patients with mucopolysaccharidosis IVA. Tapiero-Rodriguez SM The application of clinical genetics 2018 PMID: 29731656
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations. Morrone A Molecular genetics and metabolism 2014 PMID: 24726177
Mucopolysaccharidosis IVA (Morquio A syndrome) and VI (Maroteaux-Lamy syndrome): under-recognized and challenging to diagnose. Lachman RS Skeletal radiology 2014 PMID: 24389823
Mucopolysaccharidosis IVA: correlation between genotype, phenotype and keratan sulfate levels. Dũng VC Molecular genetics and metabolism 2013 PMID: 23876334
Molecular analysis of mucopolysaccharidosis IVA (Morquio A) in Spain. Pajares S Molecular genetics and metabolism 2012 PMID: 22521955
Effect of 'attenuated' mutations in mucopolysaccharidosis IVA on molecular phenotypes of N-acetylgalactosamine-6-sulfate sulfatase. Montaño AM Journal of inherited metabolic disease 2007 PMID: 17876718
Mucopolysaccharidosis IVA: identification of mutations and methylation study in GALNS gene. Tomatsu S Journal of medical genetics 2004 PMID: 15235041
Biochemical and structural analysis of missense mutations in N-acetylgalactosamine-6-sulfate sulfatase causing mucopolysaccharidosis IVA phenotypes. Sukegawa K Human molecular genetics 2000 PMID: 10814710
A novel common missense mutation G301C in the N-acetylgalactosamine-6-sulfate sulfatase gene in mucopolysaccharidosis IVA. Kato Z Human genetics 1997 PMID: 9385378
Identification of 31 novel mutations in the N-acetylgalactosamine-6-sulfatase gene reveals excessive allelic heterogeneity among patients with Morquio A syndrome. Bunge S Human mutation 1997 PMID: 9298823
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALNS - - - -
https://doi.org/10.1016/j.mgene.2018.01.008; https://doi.org/10.1590/S1415-47572007000400004; - - - -

Text-mined citations for rs118204443...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021