rs1057521800
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000444.6(PHEX):c.1739A>G(p.His580Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H580D) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000444.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHEX | NM_000444.6 | c.1739A>G | p.His580Arg | missense_variant | 17/22 | ENST00000379374.5 | |
PTCHD1-AS | NR_073010.2 | n.1048+8396T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHEX | ENST00000379374.5 | c.1739A>G | p.His580Arg | missense_variant | 17/22 | 1 | NM_000444.6 | P1 | |
PTCHD1-AS | ENST00000669979.1 | n.325+8396T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 25
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Familial X-linked hypophosphatemic vitamin D refractory rickets Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing;provider interpretation | Geisinger Autism and Developmental Medicine Institute, Geisinger Health System | Feb 23, 2018 | This variant was identified in a 5 year old female with a genetic and biochemical diagnosis of Sanfilippo syndrome. The variant is absent from the gnomAD database, and it was found to be de novo (with maternity and paternity confirmed). Computational models predict it to be deleterious. Other missense variants involving this codon (H580P) and nearby codons have been reported in the Human Gene Mutation Database. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2016 | The H580R variant in the PHEX gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. However, a missense variant at this same codon (H580P) as well as missense variants in neighboring codons (G579R, G579V, and H584P) have been reported in the Human Gene Mutation Database in association with hypophosphatemic rickets (Stenson et al., 2014), supporting the functional importance of this region of the protein. The H580R variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The H580R variant is a conservative amino acid substitution, which occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. The H580R variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at