NM_013382.7(POMT2):c.1627C>A (p.Leu543Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 29, 2018
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:: RCV000658417.1

Allele description [Variation Report for NM_013382.7(POMT2):c.1627C>A (p.Leu543Met)]

NM_013382.7(POMT2):c.1627C>A (p.Leu543Met)

Gene:

POMT2:protein O-mannosyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q24.3

Genomic location:

Preferred name:

NM_013382.7(POMT2):c.1627C>A (p.Leu543Met)

HGVS:

NC_000014.9:g.77283823G>T
NG_008897.1:g.42060C>A
NM_013382.7:c.1627C>AMANE SELECT
NP_037514.2:p.Leu543Met
NP_037514.2:p.Leu543Met
LRG_844t1:c.1627C>A
LRG_844:g.42060C>A
LRG_844p1:p.Leu543Met
NC_000014.8:g.77750166G>T
NM_013382.5:c.1627C>A

Protein change:

L543M

Links:

dbSNP: rs367552151

NCBI 1000 Genomes Browser:

rs367552151

Molecular consequence:

NM_013382.7:c.1627C>A - 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
SCV000780189	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (May 29, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000780189

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(May 29, 2018)

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, SCV000780189.1

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

Description

The L543M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The L543M variant is observed in 18/24,030 (0.075%) alleles from individuals of African background (Lek et al., 2016). This variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function.

#	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: Mar 5, 2024

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