NM_000444.6(PHEX):c.613del (p.Arg205fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 24, 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:: RCV002541818.2

Allele description [Variation Report for NM_000444.6(PHEX):c.613del (p.Arg205fs)]

NM_000444.6(PHEX):c.613del (p.Arg205fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

Xp22.11

Genomic location:

Preferred name:

NM_000444.6(PHEX):c.613del (p.Arg205fs)

HGVS:

NC_000023.11:g.22077652del
NG_007563.2:g.49850del
NM_000444.6:c.613delMANE SELECT
NM_001282754.2:c.613del
NP_000435.3:p.Arg205fs
NP_001269683.1:p.Arg205fs
NC_000023.10:g.22095769del
NC_000023.10:g.22095770del
NM_000444.5:c.613delC

Protein change:

R205fs

Links:

dbSNP: rs1929214770

NCBI 1000 Genomes Browser:

rs1929214770

Molecular consequence:

NM_000444.6:c.613del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282754.2:c.613del - 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
SCV003315253	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 24, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 34006472, 9097956, 9106524, 19219621, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003315253

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 24, 2022)

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

Exome sequencing reveals genetic architecture in patients with isolated or syndromic short stature.

Fan X, Zhao S, Yu C, Wu D, Yan Z, Fan L, Song Y, Wang Y, Li C, Ming Y, Gui B, Niu Y, Li X, Yang X, Luo S, Zhang Q, Zhao X, Pan H, Li M, Xia W, Qiu G, Liu P, et al.

J Genet Genomics. 2021 May 20;48(5):396-402. doi: 10.1016/j.jgg.2021.02.008. Epub 2021 Mar 22.

PubMed [citation]

PMID:: 34006472

Distribution of mutations in the PEX gene in families with X-linked hypophosphataemic rickets (HYP).

Rowe PS, Oudet CL, Francis F, Sinding C, Pannetier S, Econs MJ, Strom TM, Meitinger T, Garabedian M, David A, Macher MA, Questiaux E, Popowska E, Pronicka E, Read AP, Mokrzycki A, Glorieux FH, Drezner MK, Hanauer A, Lehrach H, Goulding JN, O'Riordan JL.

Hum Mol Genet. 1997 Apr;6(4):539-49.

PubMed [citation]

PMID:: 9097956

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003315253.2

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 998044). This premature translational stop signal has been observed in individual(s) with clinical features of X-linked hypophosphatemia (PMID: 34006472). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg205Valfs*16) 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).

#	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: May 7, 2024

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