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NM_000512.5(GALNS):c.1438G>T (p.Val480Phe)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
9 (Most recent: Oct 4, 2021)
Last evaluated:
Feb 1, 2021
Accession:
VCV000284192.15
Variation ID:
284192
Description:
single nucleotide variant
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NM_000512.5(GALNS):c.1438G>T (p.Val480Phe)

Allele ID
268429
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.3
Genomic location
16: 88818051 (GRCh38) GRCh38 UCSC
16: 88884459 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.88818051C>A
NC_000016.9:g.88884459C>A
NG_008667.1:g.43916G>T
... more HGVS
Protein change
V480F, V295F, V486F
Other names
-
Canonical SPDI
NC_000016.10:88818050:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00739 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00134
The Genome Aggregation Database (gnomAD) 0.00557
Trans-Omics for Precision Medicine (TOPMed) 0.00591
The Genome Aggregation Database (gnomAD) 0.00596
Exome Aggregation Consortium (ExAC) 0.00286
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00588
1000 Genomes Project 0.00739
Links
ClinGen: CA8234665
dbSNP: rs151296605
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Feb 1, 2021 RCV001087801.6
Benign 2 criteria provided, single submitter Nov 6, 2015 RCV000314283.3
Benign 3 criteria provided, single submitter Feb 14, 2020 RCV000675526.7
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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
674 818

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 06, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000336713.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-IV-A
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001277428.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Nov 05, 2020)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-IV-A
Allele origin: germline
Invitae
Accession: SCV000629965.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Feb 14, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001837536.1
Submitted: (Sep 07, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 25545067)
Benign
(Jan 02, 2020)
criteria provided, single submitter
Method: clinical testing
Mucopolysaccharidosis, MPS-IV-A
Allele origin: germline
Al Jalila Children's Genomics Center,Al Jalila Childrens Speciality Hospital
Accession: SCV001984019.1
Submitted: (Oct 04, 2021)
Evidence details
Likely benign
(Feb 01, 2021)
criteria provided, single submitter
Method: curation
Mucopolysaccharidosis, MPS-IV-A
Allele origin: germline
Laboratory of Diagnosis and Therapy of Lysosomal Disorders,University of Padova
Accession: SCV001547967.3
Submitted: (Feb 22, 2021)
Evidence details
Publications
PubMed (2)
Comment:
In vivo functional studies supportive of a damaging effect on the gene product (low to null enzymatic activity in homozygotes; PS3_supporting); allele frequency is greater … (more)
Uncertain significance
(Mar 16, 2017)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801217.1
Submitted: (May 23, 2018)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799953.1
Submitted: (Aug 19, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001739916.3
Submitted: (Sep 02, 2021)
Evidence details

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
Optimizing the molecular diagnosis of GALNS: novel methods to define and characterize Morquio-A syndrome-associated mutations. Caciotti A Human mutation 2015 PMID: 25545067
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GALNS - - - -

Text-mined citations for rs151296605...

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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 Nov 27, 2021