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NM_000444.6(PHEX):c.349+1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 14, 2022
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:
RCV003558624.2

Allele description [Variation Report for NM_000444.6(PHEX):c.349+1G>A]

NM_000444.6(PHEX):c.349+1G>A

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.349+1G>A
HGVS:
  • NC_000023.11:g.22047212G>A
  • NG_007563.2:g.19410G>A
  • NG_007563.3:g.19889G>A
  • NM_000444.6:c.349+1G>AMANE SELECT
  • NM_001282754.2:c.349+1G>A
  • NC_000023.10:g.22065330G>A
Links:
dbSNP: rs193922459
NCBI 1000 Genomes Browser:
rs193922459
Molecular consequence:
  • NM_000444.6:c.349+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001282754.2:c.349+1G>A - 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
SCV004299504Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 14, 2022) 		germlineclinical testing

PubMed (7)
[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

Identification of fifteen novel PHEX gene mutations in Finnish patients with hypophosphatemic rickets.

Tyynismaa H, Kaitila I, Näntö-Salonen K, Ala-Houhala M, Alitalo T.

Hum Mutat. 2000 Apr;15(4):383-4.

PubMed [citation]
PMID:
10737991

Clinical and genetic analysis in a large Chinese cohort of patients with X-linked hypophosphatemia.

Zhang C, Zhao Z, Sun Y, Xu L, JiaJue R, Cui L, Pang Q, Jiang Y, Li M, Wang O, He X, He S, Nie M, Xing X, Meng X, Zhou X, Yan L, Kaplan JM, Insogna KL, Xia W.

Bone. 2019 Apr;121:212-220. doi: 10.1016/j.bone.2019.01.021. Epub 2019 Jan 23.

PubMed [citation]
PMID:
30682568
See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004299504.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

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: 803740). Disruption of this splice site has been observed in individuals with hypophosphatemia (PMID: 10737991, 30682568). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 3 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: Sep 29, 2024