NM_013382.7(POMT2):c.1712dup (p.Ile572fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 26, 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:: RCV001009061.1

Allele description [Variation Report for NM_013382.7(POMT2):c.1712dup (p.Ile572fs)]

NM_013382.7(POMT2):c.1712dup (p.Ile572fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

14q24.3

Genomic location:

Preferred name:

NM_013382.7(POMT2):c.1712dup (p.Ile572fs)

HGVS:

NC_000014.9:g.77280406dup
NG_008897.1:g.45478dup
NM_013382.7:c.1712dupMANE SELECT
NP_037514.2:p.Ile572fs
LRG_844t1:c.1712dup
LRG_844:g.45478dup
NC_000014.8:g.77746747_77746748insG
NC_000014.8:g.77746749dup
NM_013382.5:c.1712dupC

Protein change:

I572fs

Links:

dbSNP: rs780725241

NCBI 1000 Genomes Browser:

rs780725241

Molecular consequence:

NM_013382.7:c.1712dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001168871	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Sep 26, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168871

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Sep 26, 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, SCV001168871.1

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

Description

The c.1712dupC variant in the POMT2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The 1712dupC variant causes a frameshift starting with codon Isoleucine 572, changes this amino acid to a Tyrosine residue, and creates a premature Stop codon at position 13 of the new reading frame, denoted p.Ile572TyrfsX13. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The 1712dupC variant is observed in 1/246254 (0.0004%) alleles in large population cohorts (Lek et al., 2016). We interpret 1712dupC as a likely 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: Mar 10, 2024

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