NM_018129.4(PNPO):c.685C>T (p.Arg229Trp) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 1, 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:: RCV003231091.1

Allele description [Variation Report for NM_018129.4(PNPO):c.685C>T (p.Arg229Trp)]

NM_018129.4(PNPO):c.685C>T (p.Arg229Trp)

Gene:

PNPO:pyridoxamine 5'-phosphate oxidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.32

Genomic location:

Preferred name:

NM_018129.4(PNPO):c.685C>T (p.Arg229Trp)

HGVS:

NC_000017.11:g.47946681C>T
NG_008744.1:g.10159C>T
NM_018129.3:c.685C>T
NM_018129.4:c.685C>TMANE SELECT
NP_060599.1:p.Arg229Trp
NC_000017.10:g.46024047C>T
Q9NVS9:p.Arg229Trp

Protein change:

R229W; ARG229TRP

Links:

UniProtKB: Q9NVS9#VAR_029360; OMIM: 603287.0001; dbSNP: rs104894629

NCBI 1000 Genomes Browser:

rs104894629

Molecular consequence:

NM_018129.4:c.685C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV003929582	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 1, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003929582

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Dec 1, 2022)

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, SCV003929582.1

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

Description

Published functional studies demonstrate a damaging effect on enzymatic efficiency (Mills et al., 2005; Musayev et al., 2009; Mills et al., 2014); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 15772097, 30671974, 25546381, 23500531, 33421502, 32888189, 19759001, 27419045, 24645144, 32788630, 28133863, 23708187, 25762494, 24266778, 18485777, 26535729, 34769443, 28985901)

#	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: Sep 29, 2024

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