rs606231182
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_016032.4(ZDHHC9):c.172_175del(p.Arg58ThrfsTer26) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 22)
Consequence
ZDHHC9
NM_016032.4 frameshift
NM_016032.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.60
Genes affected
ZDHHC9 (HGNC:18475): (zinc finger DHHC-type palmitoyltransferase 9) This gene encodes an integral membrane protein that is a member of the zinc finger DHHC domain-containing protein family. The encoded protein forms a complex with golgin subfamily A member 7 and functions as a palmitoyltransferase. This protein specifically palmitoylates HRAS and NRAS. Mutations in this gene are associated with X-linked cognitive disability. Alternate splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-129829133-TAGCG-T is Pathogenic according to our data. Variant chrX-129829133-TAGCG-T is described in ClinVar as [Pathogenic]. Clinvar id is 10709.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-129829133-TAGCG-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC9 | NM_016032.4 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 4/11 | ENST00000357166.11 | |
ZDHHC9 | NM_001008222.3 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 3/10 | ||
ZDHHC9 | XM_011531348.4 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 4/6 | ||
ZDHHC9 | XM_047442151.1 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC9 | ENST00000357166.11 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 4/11 | 1 | NM_016032.4 | P1 | |
ZDHHC9 | ENST00000371064.7 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 3/10 | 1 | P1 | ||
ZDHHC9 | ENST00000406492.2 | c.172_175del | p.Arg58ThrfsTer26 | frameshift_variant | 3/5 | 5 | |||
ZDHHC9 | ENST00000433917.5 | c.51_54del | p.Arg18ThrfsTer26 | frameshift_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Syndromic X-linked intellectual disability Raymond type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2009 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at