NM_000444.6(PHEX):c.1604C>T (p.Thr535Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 18, 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:: RCV003734697.2

Allele description [Variation Report for NM_000444.6(PHEX):c.1604C>T (p.Thr535Met)]

NM_000444.6(PHEX):c.1604C>T (p.Thr535Met)

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.1604C>T (p.Thr535Met)

HGVS:

NC_000023.11:g.22190461C>T
NG_007563.2:g.162658C>T
NG_007563.3:g.163138C>T
NM_000444.5:c.1604C>T
NM_000444.6:c.1604C>TMANE SELECT
NM_001282754.2:c.1604C>T
NP_000435.3:p.Thr535Met
NP_001269683.1:p.Thr535Met
NC_000023.10:g.22208578C>T

Protein change:

T535M

Molecular consequence:

NM_000444.6:c.1604C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001282754.2:c.1604C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MULTISPECIES: ubiquinol-cytochrome C chaperone family protein [Pseudomonadaceae]
MULTISPECIES: ubiquinol-cytochrome C chaperone family protein [Pseudomonadaceae]
gi|489210623|ref|WP_003119448.1|

Protein
MULTISPECIES: DNA recombination protein RmuC [Pseudomonadaceae]
MULTISPECIES: DNA recombination protein RmuC [Pseudomonadaceae]
gi|1028072781|ref|WP_063837559.1|

Protein
Homo sapiens, clone IMAGE:4909007, mRNA, partial cds
Homo sapiens, clone IMAGE:4909007, mRNA, partial cds
gi|18606062|gb|BC022798.1|

Nucleotide
Atherurus macrourus isolate AM10 cytochrome b (cytb) gene, partial cds; mitochon...
Atherurus macrourus isolate AM10 cytochrome b (cytb) gene, partial cds; mitochondrial
gi|1216331592|gb|KX580790.1|

Nucleotide
H.sapiens CpG island DNA genomic Mse1 fragment, clone 62b1, reverse read cpg62b1...
H.sapiens CpG island DNA genomic Mse1 fragment, clone 62b1, reverse read cpg62b1.rt1a
gi|1038662|emb|Z65840.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004539585	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 18, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29644095, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004539585

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 18, 2023)

germline

clinical testing

PubMed (2)
[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

Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization.

Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S, Cakici JA, Benson W, Kaplan RH, Kronick R, Bainbridge MN, Friedman J, Gold JJ, Ding Y, Veeraraghavan N, Dimmock D, Kingsmore SF.

NPJ Genom Med. 2018;3:10. doi: 10.1038/s41525-018-0049-4.

PubMed [citation]

PMID:: 29644095
PMCID:: PMC5884823

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, SCV004539585.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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. 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. This missense change has been observed in individual(s) with hypophosphatemia (PMID: 29644095). This variant is present in population databases (no rsID available, gnomAD 0.001%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 535 of the PHEX protein (p.Thr535Met).

#	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: Oct 8, 2024

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