rs864309653
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_000899.5(KITLG):c.286_303delAGTAATTATTCCATCATAinsT(p.Ser96fs) variant causes a frameshift, synonymous change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. SNYSIID96*?) has been classified as Pathogenic. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
KITLG
NM_000899.5 frameshift, synonymous
NM_000899.5 frameshift, synonymous
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.61
Genes affected
KITLG (HGNC:6343): (KIT ligand) This gene encodes the ligand of the tyrosine-kinase receptor encoded by the KIT locus. This ligand is a pleiotropic factor that acts in utero in germ cell and neural cell development, and hematopoiesis, all believed to reflect a role in cell migration. In adults, it functions pleiotropically, while mostly noted for its continued requirement in hematopoiesis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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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 12-88518757-TATGATGGAATAATTACT-A is Pathogenic according to our data. Variant chr12-88518757-TATGATGGAATAATTACT-A is described in ClinVar as [Pathogenic]. Clinvar id is 218887.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KITLG | NM_000899.5 | c.286_303delAGTAATTATTCCATCATAinsT | p.Ser96fs | frameshift_variant, synonymous_variant | 4/10 | ENST00000644744.1 | NP_000890.1 | |
KITLG | NM_003994.6 | c.286_303delAGTAATTATTCCATCATAinsT | p.Ser96fs | frameshift_variant, synonymous_variant | 4/9 | NP_003985.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KITLG | ENST00000644744.1 | c.286_303delAGTAATTATTCCATCATAinsT | p.Ser96fs | frameshift_variant, synonymous_variant | 4/10 | NM_000899.5 | ENSP00000495951.1 |
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:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Autosomal dominant nonsyndromic hearing loss 69 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 05, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at