NM_000303.3(PMM2):c.310C>G (p.Leu104Val) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 10, 2015
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:: RCV000437277.1

Allele description [Variation Report for NM_000303.3(PMM2):c.310C>G (p.Leu104Val)]

NM_000303.3(PMM2):c.310C>G (p.Leu104Val)

Gene:

PMM2:phosphomannomutase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NM_000303.3(PMM2):c.310C>G (p.Leu104Val)

HGVS:

NC_000016.10:g.8806370C>G
NG_009209.1:g.13558C>G
NM_000303.3:c.310C>GMANE SELECT
NP_000294.1:p.Leu104Val
NC_000016.9:g.8900227C>G
NM_000303.2:c.310C>G

Protein change:

L104V

Links:

dbSNP: rs770458492

NCBI 1000 Genomes Browser:

rs770458492

Molecular consequence:

NM_000303.3:c.310C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000515964	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 10, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000515964

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 10, 2015)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000515964.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The L104V variant was not observed in approximately 6,500 individuals of European and AfricanAmerican ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variantin these populations. This substitution occurs at a position that is conserved across species. In silicoanalysis predict this variant is probably damaging to the protein structure/function. Missense variants innearby residues (N101K, Y102C, C103F, Y106C, Y106F, A108V, P113A, P113L) have been reported inthe Human Gene Mutation Database in association with congenital disorder of glycosylation type Ia(CDG1A) (Stenson et al., 2014), supporting the functional importance of this region of the protein.Therefore, this variant is interpreted as a pathogenic variant.

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

Last Updated: Sep 29, 2024

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