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NM_000528.4(MAN2B1):c.685C>T (p.Arg229Trp)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Nov 10, 2021)
Last evaluated:
Sep 5, 2021
Accession:
VCV000208258.4
Variation ID:
208258
Description:
single nucleotide variant
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NM_000528.4(MAN2B1):c.685C>T (p.Arg229Trp)

Allele ID
204512
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 12663781 (GRCh38) GRCh38 UCSC
19: 12774595 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.12774595G>A
NC_000019.10:g.12663781G>A
NG_008318.1:g.7997C>T
... more HGVS
Protein change
R229W
Other names
-
Canonical SPDI
NC_000019.10:12663780:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA350933
UniProtKB: O00754#VAR_068042
dbSNP: rs763257568
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Sep 5, 2021 RCV000206936.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MAN2B1 - - GRCh38
GRCh37
633 653

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 10, 2017)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: unknown
Counsyl
Accession: SCV000800761.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (3)
Pathogenic
(Jan 20, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Invitae
Accession: SCV001225168.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces arginine with tryptophan at codon 229 of the MAN2B1 protein (p.Arg229Trp). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(Sep 05, 2021)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Nilou-Genome Lab
Accession: SCV002014509.1
Submitted: (Nov 10, 2021)
Evidence details
Uncertain significance
(Jun 07, 2012)
no assertion criteria provided
Method: literature only
Deficiency of alpha-mannosidase
Allele origin: germline
ClinVar Staff, National Center for Biotechnology Information (NCBI)
Accession: SCV000243964.1
Submitted: (Aug 25, 2015)
Evidence details
Publications
PubMed (1)
Other databases
http://web.expasy.org/variant_pa…

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
Alpha-mannosidosis: correlation between phenotype, genotype and mutant MAN2B1 subcellular localisation. Borgwardt L Orphanet journal of rare diseases 2015 PMID: 26048034
Identification of 83 novel alpha-mannosidosis-associated sequence variants: functional analysis of MAN2B1 missense mutations. Riise Stensland HM Human mutation 2012 PMID: 22161967
Molecular and cellular characterization of novel {alpha}-mannosidosis mutations. Kuokkanen E Human molecular genetics 2011 PMID: 21505070
alpha-Mannosidosis in the guinea pig: cloning of the lysosomal alpha-mannosidase cDNA and identification of a missense mutation causing alpha-mannosidosis. Berg T Biochimica et biophysica acta 2002 PMID: 11959458
http://web.expasy.org/variant_pages/VAR_068042.html - - - -

Text-mined citations for rs763257568...

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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