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NM_000444.6(PHEX):c.750del (p.Leu249_Tyr250insTer) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 28, 2019
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:
RCV001066122.9

Allele description [Variation Report for NM_000444.6(PHEX):c.750del (p.Leu249_Tyr250insTer)]

NM_000444.6(PHEX):c.750del (p.Leu249_Tyr250insTer)

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.750del (p.Leu249_Tyr250insTer)
HGVS:
  • NC_000023.11:g.22094000del
  • NG_007563.2:g.66198del
  • NM_000444.6:c.750delMANE SELECT
  • NM_001282754.2:c.750del
  • NP_000435.3:p.Leu249_Tyr250insTer
  • NP_001269683.1:p.Leu249_Tyr250insTer
  • NC_000023.10:g.22112118del
  • NM_000444.5:c.750del
Links:
dbSNP: rs1930018183
NCBI 1000 Genomes Browser:
rs1930018183
Molecular consequence:
  • NM_000444.6:c.750del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001282754.2:c.750del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001231119Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 28, 2019) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

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
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001231119.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PHEX are known to be pathogenic (PMID: 9097956, 9106524, 19219621). A different variant (c.750C>A) giving rise to the same protein effect observed here (p.Tyr250*) has been determined to be pathogenic (PMID: 9768674). This suggests that this variant is also likely to be causative of disease. This variant has been observed in individual(s) with clinical features of hypophosphatemia (Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Tyr250*) in the PHEX gene. It is expected to result in an absent or disrupted protein product.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024