NM_000528.4(MAN2B1):c.1164G>A (p.Trp388Ter) AND Deficiency of alpha-mannosidase

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 10, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003601009.2

Allele description [Variation Report for NM_000528.4(MAN2B1):c.1164G>A (p.Trp388Ter)]

NM_000528.4(MAN2B1):c.1164G>A (p.Trp388Ter)

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.1164G>A (p.Trp388Ter)

HGVS:

NC_000019.10:g.12658290C>T
NG_008318.1:g.13488G>A
NM_000528.4:c.1164G>AMANE SELECT
NM_001173498.2:c.1161G>A
NP_000519.2:p.Trp388Ter
NP_001166969.1:p.Trp387Ter
NC_000019.9:g.12769104C>T

Protein change:

W387*

Molecular consequence:

NM_000528.4:c.1164G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001173498.2:c.1161G>A - nonsense - [Sequence Ontology: SO:0001587]

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

Recent activity

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CBSU8184.fwd NICHD_XGC_tropLimb_m Xenopus tropicalis cDNA clone IMAGE:8870455 5'...
CBSU8184.fwd NICHD_XGC_tropLimb_m Xenopus tropicalis cDNA clone IMAGE:8870455 5', mRNA sequence
gi|126596151|gnl|dbEST|45105831|gb| 472.1|

Nucleotide
AGENCOURT_8148900 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:5570079 5', mRN...
AGENCOURT_8148900 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:5570079 5', mRNA sequence
gi|21874672|gnl|dbEST|12887489|gb|B 75.1|

Nucleotide
JGI_XZT700.rev NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone XZT700 3', mRNA se...
JGI_XZT700.rev NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone XZT700 3', mRNA sequence
gi|57128054|gnl|dbEST|26981359|gb|C 95.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004520265	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 10, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9915946, 22161967, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004520265

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 10, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Spectrum of mutations in alpha-mannosidosis.

Berg T, Riise HM, Hansen GM, Malm D, Tranebjaerg L, Tollersrud OK, Nilssen O.

Am J Hum Genet. 1999 Jan;64(1):77-88.

PubMed [citation]

PMID:: 9915946
PMCID:: PMC1377705

Identification of 83 novel alpha-mannosidosis-associated sequence variants: functional analysis of MAN2B1 missense mutations.

Riise Stensland HM, Klenow HB, Van Nguyen L, Hansen GM, Malm D, Nilssen Ø.

Hum Mutat. 2012 Mar;33(3):511-20. doi: 10.1002/humu.22005. Epub 2012 Jan 23. Erratum in: Hum Mutat. 2016 Aug;37(8):827. doi: 10.1002/humu.23002.

PubMed [citation]

PMID:: 22161967

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004520265.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant has not been reported in the literature in individuals affected with MAN2B1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp388*) in the MAN2B1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MAN2B1 are known to be pathogenic (PMID: 9915946, 22161967). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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