NM_000291.4(PGK1):c.185G>A (p.Ser62Asn) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 21, 2016
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:: RCV000417927.1

Allele description [Variation Report for NM_000291.4(PGK1):c.185G>A (p.Ser62Asn)]

NM_000291.4(PGK1):c.185G>A (p.Ser62Asn)

Gene:

PGK1:phosphoglycerate kinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq21.1

Genomic location:

Preferred name:

NM_000291.4(PGK1):c.185G>A (p.Ser62Asn)

HGVS:

NC_000023.11:g.78113812G>A
NG_008862.1:g.14644G>A
NM_000291.4:c.185G>AMANE SELECT
NP_000282.1:p.Ser62Asn
NC_000023.10:g.77369309G>A
NM_000291.3:c.185G>A

Protein change:

S62N

Links:

dbSNP: rs1057524140

NCBI 1000 Genomes Browser:

rs1057524140

Molecular consequence:

NM_000291.4:c.185G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000534674	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Dec 21, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000534674

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Dec 21, 2016)

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, SCV000534674.4

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

Description

The S62N variant in the PGK1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The S62N variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The S62N variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. The S62N variant is a strong candidate for 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: Apr 23, 2022

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