NM_000444.6(PHEX):c.10G>C (p.Glu4Gln) AND Familial X-linked hypophosphatemic vitamin D refractory rickets

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Apr 27, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000366699.2

Allele description [Variation Report for NM_000444.6(PHEX):c.10G>C (p.Glu4Gln)]

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

Gene:
PHEX:phosphate regulating endopeptidase homolog X-linked [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.11
Genomic location:
Preferred name:
NM_000444.6(PHEX):c.10G>C (p.Glu4Gln)
HGVS:
  • NC_000023.11:g.22033015G>C
  • NG_007563.2:g.5213G>C
  • NM_000444.6:c.10G>CMANE SELECT
  • NM_001282754.2:c.10G>C
  • NP_000435.3:p.Glu4Gln
  • NP_001269683.1:p.Glu4Gln
  • NC_000023.10:g.22051133G>C
  • NM_000444.4:c.10G>C
  • NM_000444.5:c.10G>C
  • p.GLU4GLN
Protein change:
E4Q
Links:
dbSNP: rs147859619
NCBI 1000 Genomes Browser:
rs147859619
Molecular consequence:
  • NM_000444.6:c.10G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001282754.2:c.10G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial X-linked hypophosphatemic vitamin D refractory rickets (XLHR)
Synonyms:
HYPOPHOSPHATEMIC VITAMIN D-RESISTANT RICKETS; Hypophosphatemic Rickets, X-Linked Dominant; Hypophosphatemia, vitamin D-resistant rickets; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010619; MedGen: C0733682; Orphanet: 89936; OMIM: 307800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000267446Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Centercriteria provided, single submitter
Uncertain significance
(Mar 18, 2016)
germlinereference population

PubMed (1)
[See all records that cite this PMID]

SCV000482137Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
East Asiangermlineunknown1not providednot providednot providednot providedreference population

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center, SCV000267446.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1East Asian1not providednot providedreference population PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV000482137.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Last Updated: Nov 27, 2021

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