rs878854420
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM5PP2PP5_Moderate
The NM_017934.7(PHIP):c.50T>G(p.Phe17Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000000693 in 1,442,510 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. F17S) has been classified as Likely pathogenic.
Frequency
Consequence
NM_017934.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHIP | NM_017934.7 | c.50T>G | p.Phe17Cys | missense_variant | 2/40 | ENST00000275034.5 | |
PHIP | XM_005248729.6 | c.50T>G | p.Phe17Cys | missense_variant | 2/40 | ||
PHIP | XM_011535919.2 | c.50T>G | p.Phe17Cys | missense_variant | 2/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHIP | ENST00000275034.5 | c.50T>G | p.Phe17Cys | missense_variant | 2/40 | 1 | NM_017934.7 | P3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.93e-7 AC: 1AN: 1442510Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 716076
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.