chr12-119876130-ATCCAAAGGAT-A
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_001206999.2(CIT):c.29_38del(p.Asn10MetfsTer15) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
CIT
NM_001206999.2 frameshift
NM_001206999.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.06
Genes affected
CIT (HGNC:1985): (citron rho-interacting serine/threonine kinase) This gene encodes a serine/threonine-protein kinase that functions in cell division. Together with the kinesin KIF14, this protein localizes to the central spindle and midbody, and functions to promote efficient cytokinesis. This protein is involved in central nervous system development. Polymorphisms in this gene are associated with bipolar disorder and risk for schizophrenia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 14 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-119876130-ATCCAAAGGAT-A is Pathogenic according to our data. Variant chr12-119876130-ATCCAAAGGAT-A is described in ClinVar as [Pathogenic]. Clinvar id is 221283.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIT | NM_001206999.2 | c.29_38del | p.Asn10MetfsTer15 | frameshift_variant | 2/48 | ENST00000392521.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIT | ENST00000392521.7 | c.29_38del | p.Asn10MetfsTer15 | frameshift_variant | 2/48 | 1 | NM_001206999.2 | P1 | |
CIT | ENST00000261833.11 | c.29_38del | p.Asn10MetfsTer15 | frameshift_variant | 2/47 | 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:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Microcephaly 17, primary, autosomal recessive Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 02, 2016 | - - |
Autosomal recessive primary microcephaly Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Sbielas Lab-Department of Human Genetics University of Michigan, University of Michigan Medical School | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at