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NM_000528.4(MAN2B1):c.455A>G (p.Asn152Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Nov 10, 2021)
Last evaluated:
Sep 5, 2021
Accession:
VCV000786791.7
Variation ID:
786791
Description:
single nucleotide variant
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NM_000528.4(MAN2B1):c.455A>G (p.Asn152Ser)

Allele ID
716176
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 12664967 (GRCh38) GRCh38 UCSC
19: 12775781 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.12775781T>C
NC_000019.10:g.12664967T>C
NG_008318.1:g.6811A>G
... more HGVS
Protein change
N152S
Other names
-
Canonical SPDI
NC_000019.10:12664966:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00019
Exome Aggregation Consortium (ExAC) 0.00021
1000 Genomes Project 0.00040
Trans-Omics for Precision Medicine (TOPMed) 0.00071
The Genome Aggregation Database (gnomAD) 0.00089
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00054
Links
dbSNP: rs200164758
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Apr 17, 2019 RCV001766798.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Sep 5, 2021 RCV000968907.6
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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
631 651

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001287904.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Nov 06, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Invitae
Accession: SCV001116391.3
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Apr 17, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001991904.1
Submitted: (Oct 31, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our … (more)
Likely benign
(Sep 05, 2021)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Nilou-Genome Lab
Accession: SCV002014553.1
Submitted: (Nov 10, 2021)
Evidence details
Uncertain significance
(Jan 24, 2020)
no assertion criteria provided
Method: clinical testing
Alpha-mannosidosis
Allele origin: germline
Natera, Inc.
Accession: SCV001455947.1
Submitted: (Dec 28, 2020)
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs200164758...

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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 12, 2021