NM_000292.3(PHKA2):c.1144dup (p.Glu382fs) 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:: RCV001008374.1

Allele description [Variation Report for NM_000292.3(PHKA2):c.1144dup (p.Glu382fs)]

NM_000292.3(PHKA2):c.1144dup (p.Glu382fs)

Gene:

PHKA2:phosphorylase kinase regulatory subunit alpha 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xp22.13

Genomic location:

Preferred name:

NM_000292.3(PHKA2):c.1144dup (p.Glu382fs)

HGVS:

NC_000023.11:g.18931742dup
NG_016622.1:g.57621dup
NM_000292.3:c.1144dupMANE SELECT
NP_000283.1:p.Glu382fs
NC_000023.10:g.18949860dup
NM_000292.2:c.1144dupG

Protein change:

E382fs

Links:

dbSNP: rs1601748177

NCBI 1000 Genomes Browser:

rs1601748177

Molecular consequence:

NM_000292.3:c.1144dup - 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
SCV001168142	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

SCV001168142

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, SCV001168142.1

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

Description

A variant that is likely pathogenic has been identified in the PHKA2 gene. The c.1144dupG variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.1144dupG variant causes a frameshift starting with codon Glutamic acid 382, changes this amino acid to a Glycine residue and creates a premature Stop codon at position 41 of the new reading frame, denoted p.Glu382GlyfsX41. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1144dupG variant is not observed in large population cohorts (Lek et al., 2016). Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

#	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 16, 2024

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