VCV002117393.3 - ClinVar

NM_000444.6(PHEX):c.1559G>A (p.Trp520Ter)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic/Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000444.6(PHEX):c.1559G>A (p.Trp520Ter)

Variation ID: 2117393 Accession: VCV002117393.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xp22.11 X: 22178349 (GRCh38) [ NCBI UCSC ] X: 22196466 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	Feb 20, 2024	Feb 7, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000444.6:c.1559G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000435.3:p.Trp520Ter	nonsense
NM_000444.5:c.1559G>A
NM_001282754.2:c.1559G>A	NP_001269683.1:p.Trp520Ter	nonsense
NC_000023.11:g.22178349G>A
NC_000023.10:g.22196466G>A
NG_007563.2:g.150546G>A
NG_007563.3:g.151026G>A

... more HGVS ... less HGVS

Protein change

W520*

Other names

Canonical SPDI

NC_000023.11:22178348:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PHEX		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	857	1512

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Pathogenic (1)	criteria provided, single submitter	Jun 12, 2022	RCV003039178.3
PHEX-related disorder	Likely pathogenic (1)	criteria provided, single submitter	Feb 7, 2023	RCV003395567.4

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Feb 07, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	PHEX-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004112477.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The PHEX c.1559G>A variant is predicted to result in premature protein termination (p.Trp520). To our knowledge, this variant has not been reported in the literature … (more) The PHEX c.1559G>A variant is predicted to result in premature protein termination (p.Trp520). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in PHEX are expected to be pathogenic. This variant is interpreted as likely pathogenic. (less)
Pathogenic (Jun 12, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003333330.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Publications: PubMed (3) PubMed: 9097956‚ 9106524‚ 19219621 Comment: This variant has not been reported in the literature in individuals affected with PHEX-related conditions. For these reasons, this variant has been classified as Pathogenic. … (more) This variant has not been reported in the literature in individuals affected with PHEX-related conditions. For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp520*) 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). (less)

Comment:

The PHEX c.1559G>A variant is predicted to result in premature protein termination (p.Trp520*). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in PHEX are expected to be pathogenic. This variant is interpreted as likely pathogenic.

Comment:

This variant has not been reported in the literature in individuals affected with PHEX-related conditions. For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp520*) 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).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
PHEX analysis in 118 pedigrees reveals new genetic clues in hypophosphatemic rickets.	Gaucher C	Human genetics	2009	PMID: 19219621
Mutational analysis of the PEX gene in patients with X-linked hypophosphatemic rickets.	Holm IA	American journal of human genetics	1997	PMID: 9106524
Distribution of mutations in the PEX gene in families with X-linked hypophosphataemic rickets (HYP).	Rowe PS	Human molecular genetics	1997	PMID: 9097956

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_000444.6(PHEX):c.1559G>A (p.Trp520Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...