NM_018444.4(PDP1):c.1601A>G (p.Gln534Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 12, 2022
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:: RCV001902588.4

Allele description [Variation Report for NM_018444.4(PDP1):c.1601A>G (p.Gln534Arg)]

NM_018444.4(PDP1):c.1601A>G (p.Gln534Arg)

Gene:

PDP1:pyruvate dehydrogenase phosphatase catalytic subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q22.1

Genomic location:

Preferred name:

NM_018444.4(PDP1):c.1601A>G (p.Gln534Arg)

HGVS:

NC_000008.11:g.93923660A>G
NG_012233.1:g.11727A>G
NM_001161779.2:c.1676A>G
NM_001161780.2:c.1676A>G
NM_001161781.2:c.1601A>G
NM_018444.4:c.1601A>GMANE SELECT
NP_001155251.1:p.Gln559Arg
NP_001155252.1:p.Gln559Arg
NP_001155253.1:p.Gln534Arg
NP_060914.2:p.Gln534Arg
NC_000008.10:g.94935888A>G

Protein change:

Q534R

Links:

dbSNP: rs2130392398

NCBI 1000 Genomes Browser:

rs2130392398

Molecular consequence:

NM_001161779.2:c.1676A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001161780.2:c.1676A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001161781.2:c.1601A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_018444.4:c.1601A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PREDICTED: Homo sapiens solute carrier family 36 member 1 (SLC36A1), transcript ...
PREDICTED: Homo sapiens solute carrier family 36 member 1 (SLC36A1), transcript variant X12, mRNA
gi|2217355044|ref|XM_011537592.3|

Nucleotide
Homo sapiens
Homo sapiens

Genome
Genome Links for Protein (Select 767937600) (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002141214	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002141214

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 12, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002141214.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1376060). This variant has not been reported in the literature in individuals affected with PDP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 534 of the PDP1 protein (p.Gln534Arg).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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