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NM_000444.6(PHEX):c.663+1G>T AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 3, 2023
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:
RCV001869828.3

Allele description

NM_000444.6(PHEX):c.663+1G>T

Gene:
PHEX:phosphate regulating endopeptidase X-linked [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.11
Genomic location:
Preferred name:
NM_000444.6(PHEX):c.663+1G>T
HGVS:
  • NC_000023.11:g.22077703G>T
  • NG_007563.2:g.49901G>T
  • NG_007563.3:g.50380G>T
  • NM_000444.6:c.663+1G>TMANE SELECT
  • NM_001282754.2:c.663+1G>T
  • NC_000023.10:g.22095821G>T
Links:
dbSNP: rs1556020845
NCBI 1000 Genomes Browser:
rs1556020845
Molecular consequence:
  • NM_000444.6:c.663+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001282754.2:c.663+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002245485Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 3, 2023) 		germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Novel PHEX Gene Mutation in a Patient with Sporadic Hypophosphatemic Rickets.

Kang YE, Hong JH, Kim J, Joung KH, Kim HJ, Ku BJ, Kim KS.

Endocrinol Metab (Seoul). 2014 Jun;29(2):195-201. doi: 10.3803/EnM.2014.29.2.195. Epub 2014 Jun 26.

PubMed [citation]
PMID:
25031893
PMCID:
PMC4091495

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV002245485.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1339459). Disruption of this splice site has been observed in individuals with hypophosphatemic rickets (PMID: 25031893; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 5 of the PHEX gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PHEX are known to be pathogenic (PMID: 9097956, 9106524, 19219621).

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

Last Updated: May 7, 2024