rs369178019
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_001039591.3(USP9X):āc.4163A>Gā(p.Asn1388Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000065 in 1,199,715 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001039591.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
USP9X | NM_001039591.3 | c.4163A>G | p.Asn1388Ser | missense_variant | 28/45 | ENST00000378308.7 | NP_001034680.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP9X | ENST00000378308.7 | c.4163A>G | p.Asn1388Ser | missense_variant | 28/45 | 5 | NM_001039591.3 | ENSP00000367558 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000188 AC: 21AN: 111987Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34147
GnomAD3 exomes AF: 0.000103 AC: 18AN: 175441Hom.: 0 AF XY: 0.0000647 AC XY: 4AN XY: 61803
GnomAD4 exome AF: 0.0000524 AC: 57AN: 1087728Hom.: 0 Cov.: 28 AF XY: 0.0000481 AC XY: 17AN XY: 353670
GnomAD4 genome AF: 0.000188 AC: 21AN: 111987Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34147
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 06, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2015 | - - |
Intellectual disability, X-linked 99;C4225416:Intellectual disability, X-linked 99, syndromic, female-restricted Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
USP9X-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 17, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at