10-63209240-TAACAA-TAACAAAACAAAACAAAACAACAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032776.3(JMJD1C):c.2695-6_2695-5insGTTTTGTTTTGTTTTGTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
JMJD1C
NM_032776.3 splice_region, splice_polypyrimidine_tract, intron
NM_032776.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.316
Genes affected
JMJD1C (HGNC:12313): (jumonji domain containing 1C) The protein encoded by this gene interacts with thyroid hormone receptors and contains a jumonji domain. It is a candidate histone demethylase and is thought to be a coactivator for key transcription factors. It plays a role in the DNA-damage response pathway by demethylating the mediator of DNA damage checkpoint 1 (MDC1) protein, and is required for the survival of acute myeloid leukemia. Mutations in this gene are associated with Rett syndrome and intellectual disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JMJD1C | NM_032776.3 | c.2695-6_2695-5insGTTTTGTTTTGTTTTGTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000399262.7 | NP_116165.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JMJD1C | ENST00000399262.7 | c.2695-6_2695-5insGTTTTGTTTTGTTTTGTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_032776.3 | ENSP00000382204 | ||||
JMJD1C | ENST00000542921.5 | c.2149-6_2149-5insGTTTTGTTTTGTTTTGTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | ENSP00000444682 | P1 | ||||
JMJD1C | ENST00000402544.5 | n.2667-6_2667-5insGTTTTGTTTTGTTTTGTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at