rs398122889
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM4PP3PP5_Moderate
The NM_003036.4(SKI):c.283_291del(p.Asp95_Ser97del) variant causes a inframe deletion 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 (★).
Frequency
Genomes: not found (cov: 32)
Consequence
SKI
NM_003036.4 inframe_deletion
NM_003036.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.08
Genes affected
SKI (HGNC:10896): (SKI proto-oncogene) This gene encodes the nuclear protooncogene protein homolog of avian sarcoma viral (v-ski) oncogene. It functions as a repressor of TGF-beta signaling, and may play a role in neural tube development and muscle differentiation. [provided by RefSeq, Oct 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_003036.4.
PP3
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
Variant 1-2229045-GTCCGACCGC-G is Pathogenic according to our data. Variant chr1-2229045-GTCCGACCGC-G is described in ClinVar as [Pathogenic]. Clinvar id is 37263.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-2229045-GTCCGACCGC-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SKI | NM_003036.4 | c.283_291del | p.Asp95_Ser97del | inframe_deletion | 1/7 | ENST00000378536.5 | NP_003027.1 | |
SKI | XM_005244775.4 | c.283_291del | p.Asp95_Ser97del | inframe_deletion | 1/7 | XP_005244832.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SKI | ENST00000378536.5 | c.283_291del | p.Asp95_Ser97del | inframe_deletion | 1/7 | 1 | NM_003036.4 | ENSP00000367797 | P1 | |
SKI | ENST00000704337.1 | n.137+1525_137+1533del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Shprintzen-Goldberg syndrome Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2012 | - - |
Pathogenic, criteria provided, single submitter | research | Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at