rs121918128
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_019892.6(INPP5E):c.1688G>A(p.Arg563His) variant causes a missense change. The variant allele was found at a frequency of 0.0000148 in 1,556,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_019892.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INPP5E | NM_019892.6 | c.1688G>A | p.Arg563His | missense_variant | Exon 9 of 10 | ENST00000371712.4 | NP_063945.2 | |
INPP5E | NM_001318502.2 | c.1685G>A | p.Arg562His | missense_variant | Exon 9 of 10 | NP_001305431.1 | ||
INPP5E | XM_017014926.2 | c.1688G>A | p.Arg563His | missense_variant | Exon 9 of 10 | XP_016870415.1 | ||
INPP5E | XM_047423603.1 | c.1685G>A | p.Arg562His | missense_variant | Exon 9 of 10 | XP_047279559.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INPP5E | ENST00000371712.4 | c.1688G>A | p.Arg563His | missense_variant | Exon 9 of 10 | 1 | NM_019892.6 | ENSP00000360777.3 | ||
INPP5E | ENST00000676019.1 | c.1586G>A | p.Arg529His | missense_variant | Exon 9 of 10 | ENSP00000501984.1 | ||||
INPP5E | ENST00000674693.1 | n.205G>A | non_coding_transcript_exon_variant | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000614 AC: 1AN: 162982Hom.: 0 AF XY: 0.0000116 AC XY: 1AN XY: 85978
GnomAD4 exome AF: 0.0000157 AC: 22AN: 1404116Hom.: 0 Cov.: 34 AF XY: 0.0000202 AC XY: 14AN XY: 692912
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
Joubert syndrome 1 Pathogenic:2
PP1,PM3,PM2,PM5 -
- -
Joubert syndrome and related disorders Pathogenic:1
Variant summary: INPP5E c.1688G>A (p.Arg563His) results in a non-conservative amino acid change located in the Inositol polyphosphate-related phosphatase (IPR000300) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.1e-06 in 162982 control chromosomes. c.1688G>A has been reported in the literature in at-least two individuals affected with Joubert Syndrome (Bielas_2009, Travaglini_2013). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in about 50% of normal INPP5E activity in HEK29T cells (Bielas_2009). The following publications have been ascertained in the context of this evaluation (PMID: 19668216, 23386033). ClinVar contains an entry for this variant (Variation ID: 398). Based on the evidence outlined above, the variant was classified as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at