NM_000444.6:c.7_8dupGC

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_000444.6(PHEX):​c.7_8dupGC​(p.Glu4GlnfsTer29) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 21)

Consequence

PHEX
NM_000444.6 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 3.54
Variant links:
Genes affected
PHEX (HGNC:8918): (phosphate regulating endopeptidase X-linked) The protein encoded by this gene is a transmembrane endopeptidase that belongs to the type II integral membrane zinc-dependent endopeptidase family. The protein is thought to be involved in bone and dentin mineralization and renal phosphate reabsorption. Mutations in this gene cause X-linked hypophosphatemic rickets. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 452 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-22033011-A-AGC is Pathogenic according to our data. Variant chrX-22033011-A-AGC is described in ClinVar as [Pathogenic]. Clinvar id is 803735.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PHEXNM_000444.6 linkc.7_8dupGC p.Glu4GlnfsTer29 frameshift_variant Exon 1 of 22 ENST00000379374.5 NP_000435.3 P78562B4DWG8
PHEXNM_001282754.2 linkc.7_8dupGC p.Glu4GlnfsTer29 frameshift_variant Exon 1 of 21 NP_001269683.1 P78562B4DNS0B4DWG8
PHEXXM_047442159.1 linkc.7_8dupGC p.Glu4GlnfsTer29 frameshift_variant Exon 1 of 13 XP_047298115.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PHEXENST00000379374.5 linkc.7_8dupGC p.Glu4GlnfsTer29 frameshift_variant Exon 1 of 22 1 NM_000444.6 ENSP00000368682.4 P78562
PHEXENST00000684143.1 linkc.7_8dupGC p.Glu4GlnfsTer29 frameshift_variant Exon 1 of 11 ENSP00000508264.1 A0A804HLA0
PHEXENST00000475778.2 linkn.433_434dupGC non_coding_transcript_exon_variant Exon 1 of 9 5
PHEXENST00000683214.1 linkn.433_434dupGC non_coding_transcript_exon_variant Exon 1 of 2

Frequencies

GnomAD3 genomes
Cov.:
21
GnomAD4 exome
Cov.:
28
GnomAD4 genome
Cov.:
21

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Familial X-linked hypophosphatemic vitamin D refractory rickets Pathogenic:1
May 28, 2019
Mendelics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1602240890; hg19: chrX-22051129; API