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NM_000444.6(PHEX):c.10G>C (p.Glu4Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Apr 27, 2017
Accession:
VCV000225437.2
Variation ID:
225437
Description:
single nucleotide variant
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NM_000444.6(PHEX):c.10G>C (p.Glu4Gln)

Allele ID
227421
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xp22.11
Genomic location
X: 22033015 (GRCh38) GRCh38 UCSC
X: 22051133 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.22051133G>C
NC_000023.11:g.22033015G>C
NG_007563.2:g.5213G>C
... more HGVS
Protein change
E4Q
Other names
-
Canonical SPDI
NC_000023.11:22033014:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00159 (C)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00019
The Genome Aggregation Database (gnomAD) 0.00046
1000 Genomes Project 0.00159
The Genome Aggregation Database (gnomAD) 0.00030
Trans-Omics for Precision Medicine (TOPMed) 0.00057
The Genome Aggregation Database (gnomAD), exomes 0.00073
Exome Aggregation Consortium (ExAC) 0.00074
Trans-Omics for Precision Medicine (TOPMed) 0.00089
Links
ClinGen: CA10367951
dbSNP: rs147859619
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Feb 21, 2017 RCV000435979.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 27, 2017 RCV000366699.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PHEX Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
491 966

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Familial X-linked hypophosphatemic vitamin D refractory rickets
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267446.1
Submitted: (Apr 14, 2016)
Evidence details
Benign
(Feb 21, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000614441.1
Submitted: (Aug 17, 2017)
Evidence details
Publications
PubMed (1)
Likely benign
(Jul 26, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000521205.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Familial X-linked hypophosphatemic vitamin D refractory rickets
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000482137.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
Two novel PHEX mutations in Taiwanese patients with X-linked hypophosphatemic rickets. Lo FS Nephron. Physiology 2006 PMID: 16636593

Text-mined citations for rs147859619...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021