NM_000444.6(PHEX):c.1529G>C (p.Arg510Pro) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 9, 2023
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:: RCV003558647.2

Allele description [Variation Report for NM_000444.6(PHEX):c.1529G>C (p.Arg510Pro)]

NM_000444.6(PHEX):c.1529G>C (p.Arg510Pro)

Gene:

PHEX:phosphate regulating endopeptidase X-linked [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp22.11

Genomic location:

Preferred name:

NM_000444.6(PHEX):c.1529G>C (p.Arg510Pro)

HGVS:

NC_000023.11:g.22178319G>C
NG_007563.2:g.150516G>C
NM_000444.6:c.1529G>CMANE SELECT
NM_001282754.2:c.1529G>C
NP_000435.3:p.Arg510Pro
NP_001269683.1:p.Arg510Pro
NC_000023.10:g.22196436G>C
NC_000023.10:g.22196436G>C
NM_000444.5:c.1529G>C

Protein change:

R510P

Links:

dbSNP: rs915608304

NCBI 1000 Genomes Browser:

rs915608304

Molecular consequence:

NM_000444.6:c.1529G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001282754.2:c.1529G>C - 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
SCV004299519	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 9, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 14564077, 21902834, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004299519

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 9, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

X-linked hypophosphatemia in Polish patients. 1. Mutations in the PHEX gene.

Popowska E, Pronicka E, Sułek A, Jurkiewicz D, Rowe P, Rowinska E, Krajewska-Walasek M.

J Appl Genet. 2000;41(4):293-302.

PubMed [citation]

PMID:: 14564077

Genetic diagnosis of X-linked dominant Hypophosphatemic Rickets in a cohort study: tubular reabsorption of phosphate and 1,25(OH)2D serum levels are associated with PHEX mutation type.

Morey M, Castro-Feijóo L, Barreiro J, Cabanas P, Pombo M, Gil M, Bernabeu I, Díaz-Grande JM, Rey-Cordo L, Ariceta G, Rica I, Nieto J, Vilalta R, Martorell L, Vila-Cots J, Aleixandre F, Fontalba A, Soriano-Guillén L, García-Sagredo JM, García-Miñaur S, Rodríguez B, Juaristi S, et al.

BMC Med Genet. 2011 Sep 8;12:116. doi: 10.1186/1471-2350-12-116.

PubMed [citation]

PMID:: 21902834
PMCID:: PMC3189111

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004299519.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PHEX protein function. ClinVar contains an entry for this variant (Variation ID: 830034). This missense change has been observed in individual(s) with X-linked hypophosphatemia (PMID: 14564077, 21902834; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 510 of the PHEX protein (p.Arg510Pro).

#	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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Relating variation to medicine