NM_000444.6(PHEX):c.208_212del (p.Val70fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 15, 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:: RCV001219349.6

Allele description [Variation Report for NM_000444.6(PHEX):c.208_212del (p.Val70fs)]

NM_000444.6(PHEX):c.208_212del (p.Val70fs)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

Xp22.11

Genomic location:

Preferred name:

NM_000444.6(PHEX):c.208_212del (p.Val70fs)

HGVS:

NC_000023.11:g.22047065GTAAA[1]
NG_007563.2:g.19263GTAAA[1]
NM_000444.6:c.208_212delMANE SELECT
NM_001282754.2:c.208_212del
NP_000435.3:p.Val70fs
NP_001269683.1:p.Val70fs
NC_000023.10:g.22065181_22065185del
NC_000023.10:g.22065183GTAAA[1]
NM_000444.5:c.208_212del
NM_000444.6:c.208_212delGTAAAMANE SELECT

Protein change:

V70fs

Links:

dbSNP: rs1927568587

NCBI 1000 Genomes Browser:

rs1927568587

Molecular consequence:

NM_000444.6:c.208_212del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282754.2:c.208_212del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001391284	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 15, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 9106524, 19219621, 9097956, 26377240, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001391284

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 15, 2023)

germline

clinical testing

PubMed (5)
[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

Mutational analysis of the PEX gene in patients with X-linked hypophosphatemic rickets.

Holm IA, Huang X, Kunkel LM.

Am J Hum Genet. 1997 Apr;60(4):790-7.

PubMed [citation]

PMID:: 9106524
PMCID:: PMC1712471

PHEX analysis in 118 pedigrees reveals new genetic clues in hypophosphatemic rickets.

Gaucher C, Walrant-Debray O, Nguyen TM, Esterle L, Garabédian M, Jehan F.

Hum Genet. 2009 May;125(4):401-11. doi: 10.1007/s00439-009-0631-z. Epub 2009 Feb 15.

PubMed [citation]

PMID:: 19219621

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001391284.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Val70Serfs*7) in the PHEX gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHEX are known to be pathogenic (PMID: 9097956, 9106524, 19219621). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with hypophosphataemic rickets or bone dysplasia (PMID: 9097956, 26377240). ClinVar contains an entry for this variant (Variation ID: 948148). For these reasons, this variant has been classified as Pathogenic.

#	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: Nov 3, 2024

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