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NM_002637.4(PHKA1):c.2606+1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 16, 2017
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:
RCV000519324.1

Allele description [Variation Report for NM_002637.4(PHKA1):c.2606+1G>A]

NM_002637.4(PHKA1):c.2606+1G>A

Gene:
PHKA1:phosphorylase kinase regulatory subunit alpha 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq13.1
Genomic location:
Preferred name:
NM_002637.4(PHKA1):c.2606+1G>A
HGVS:
  • NC_000023.11:g.72609623C>T
  • NG_016599.2:g.109559G>A
  • NM_001122670.2:c.2606+1G>A
  • NM_001172436.2:c.2429+1G>A
  • NM_002637.4:c.2606+1G>AMANE SELECT
  • NC_000023.10:g.71829473C>T
  • NM_002637.3:c.2606+1G>A
Links:
dbSNP: rs373517016
NCBI 1000 Genomes Browser:
rs373517016
Molecular consequence:
  • NM_001122670.2:c.2606+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001172436.2:c.2429+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_002637.4:c.2606+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000621563GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Oct 16, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000621563.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.2606+1G>A variant in the PHKA1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This splice site variant destroys the canonical splice donor site in intron 23. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.2606+1G>A variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.2606+1G>A as a pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024