NM_000444.6(PHEX):c.779dup (p.Leu260fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 16, 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:: RCV000275480.1

Allele description [Variation Report for NM_000444.6(PHEX):c.779dup (p.Leu260fs)]

NM_000444.6(PHEX):c.779dup (p.Leu260fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

Xp22.11

Genomic location:

Preferred name:

NM_000444.6(PHEX):c.779dup (p.Leu260fs)

HGVS:

NC_000023.11:g.22094029dup
NG_007563.2:g.66227dup
NM_000444.6:c.779dupMANE SELECT
NM_001282754.2:c.779dup
NP_000435.3:p.Leu260fs
NP_001269683.1:p.Leu260fs
NC_000023.10:g.22112147dup
NM_000444.4:c.779dupT

Protein change:

L260fs

Links:

dbSNP: rs886041569

NCBI 1000 Genomes Browser:

rs886041569

Molecular consequence:

NM_000444.6:c.779dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001282754.2:c.779dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000330250	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 16, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330250

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 16, 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, SCV000330250.4

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

Description

The c.779dupT pathogenic variant in the PHEX gene causes a frameshift starting with codon Leucine 260, changes this amino acid to a phenylalanine residue and creates a premature Stop codon at position 4 of the new reading frame, denoted p.Leu260PhefsX4. This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.779dupT variant was not observed in approximately 6500 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: Apr 23, 2022

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