NM_000444.6(PHEX):c.2193del (p.Phe731fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 18, 2016
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:: RCV000307183.1

Allele description [Variation Report for NM_000444.6(PHEX):c.2193del (p.Phe731fs)]

NM_000444.6(PHEX):c.2193del (p.Phe731fs)

Genes:

PTCHD1-AS:PTCHD1 antisense RNA (head to head) [Gene - HGNC]
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.2193del (p.Phe731fs)

HGVS:

NC_000023.11:g.22247896del
NG_007563.2:g.220093del
NM_000444.6:c.2193delMANE SELECT
NM_001282754.2:c.*28del
NP_000435.3:p.Phe731fs
NC_000023.10:g.22266013del
NC_000023.10:g.22266013delT
NM_000444.4:c.2193delT

Protein change:

F731fs

Links:

dbSNP: rs886041631

NCBI 1000 Genomes Browser:

rs886041631

Molecular consequence:

NM_001282754.2:c.*28del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000444.6:c.2193del - 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
SCV000330331	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 18, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330331

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 18, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000330331.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.2193delT pathogenic variant in the PHEX gene causes a frameshift starting with codon Phenylalanine 731, changes this amino acid to a Leucine residue and creates a premature Stop codon at position 9 of the new reading frame, denoted p.Phe731LeufsX9. This pathogenic variant is predicted to cause loss of normal protein function through protein truncation. Specifically, the last 19 correct amino acids are lost and replaced by 8 incorrect amino acids. The c.2193delT variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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