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NM_000528.4(MAN2B1):c.2865G>C (p.Thr955=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 23, 2021)
Last evaluated:
May 18, 2021
Accession:
VCV000093215.9
Variation ID:
93215
Description:
single nucleotide variant
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NM_000528.4(MAN2B1):c.2865G>C (p.Thr955=)

Allele ID
99122
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 12647291 (GRCh38) GRCh38 UCSC
19: 12758105 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.12647291C>G
NG_008318.1:g.24487G>C
NM_000528.4:c.2865G>C MANE Select NP_000519.2:p.Thr955= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:12647290:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00240 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00260
1000 Genomes Project 0.00240
The Genome Aggregation Database (gnomAD) 0.00175
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00261
Links
ClinGen: CA221085
dbSNP: rs148108322
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 4 criteria provided, multiple submitters, no conflicts May 18, 2021 RCV001079772.6
Uncertain significance 4 criteria provided, single submitter May 2, 2013 RCV000675472.5
Benign 1 no assertion criteria provided - RCV001705728.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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
Uncertain significance
(May 02, 2013)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000110947.8
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
Deficiency of alpha-mannosidase
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001284284.1
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
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Invitae
Accession: SCV001121589.3
Submitted: (Jan 07, 2021)
Evidence details
Benign
(May 18, 2021)
criteria provided, single submitter
Method: clinical testing
Deficiency of alpha-mannosidase
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001737260.1
Submitted: (Jun 15, 2021)
Evidence details
Likely benign
(Apr 12, 2017)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801161.1
Submitted: (May 23, 2018)
Evidence details
Benign
(Dec 30, 2019)
no assertion criteria provided
Method: clinical testing
Alpha-mannosidosis
Allele origin: germline
Natera, Inc.
Accession: SCV001453906.1
Submitted: (Dec 28, 2020)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001918279.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001927598.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001976086.1
Submitted: (Sep 21, 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
Identification of 83 novel alpha-mannosidosis-associated sequence variants: functional analysis of MAN2B1 missense mutations. Riise Stensland HM Human mutation 2012 PMID: 22161967
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=MAN2B1 - - - -

Text-mined citations for rs148108322...

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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