NM_000528.4(MAN2B1):c.594C>T (p.Phe198=) AND Deficiency of alpha-mannosidase

Clinical significance:Benign (Last evaluated: Dec 6, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000967729.5

Allele description [Variation Report for NM_000528.4(MAN2B1):c.594C>T (p.Phe198=)]

NM_000528.4(MAN2B1):c.594C>T (p.Phe198=)

Gene:
MAN2B1:mannosidase alpha class 2B member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_000528.4(MAN2B1):c.594C>T (p.Phe198=)
HGVS:
  • NC_000019.10:g.12664828G>A
  • NG_008318.1:g.6950C>T
  • NG_015814.1:g.3025G>A
  • NM_000528.4:c.594C>TMANE SELECT
  • NM_001173498.1:c.594C>T
  • NP_000519.2:p.Phe198=
  • NP_001166969.1:p.Phe198=
  • NC_000019.9:g.12775642G>A
  • NM_000528.3:c.594C>T
Links:
dbSNP: rs371341958
NCBI 1000 Genomes Browser:
rs371341958
Molecular consequence:
  • NM_000528.4:c.594C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001173498.1:c.594C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Deficiency of alpha-mannosidase (MANSA)
Synonyms:
Lysosomal alpha-D-mannosidase deficiency; Alpha mannosidase B deficiency; Mannosidosis, alpha B lysosomal; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009561; MedGen: C0024748; Orphanet: 61; OMIM: 248500

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001115146Invitaecriteria provided, single submitter
Benign
(Dec 6, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001287902Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Apr 28, 2017)
germlineclinical testing

Citation Link,

SCV001454365Natera, Inc.no assertion criteria providedBenign
(Sep 16, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001115146.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV001287902.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001454365.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 14, 2021

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