chr13-24884083-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_018451.5(CENPJ):c.3704A>G(p.Glu1235Gly) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E1235V) has been classified as Pathogenic.
Frequency
Consequence
NM_018451.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CENPJ | NM_018451.5 | c.3704A>G | p.Glu1235Gly | missense_variant, splice_region_variant | 16/17 | ENST00000381884.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CENPJ | ENST00000381884.9 | c.3704A>G | p.Glu1235Gly | missense_variant, splice_region_variant | 16/17 | 1 | NM_018451.5 | P1 | |
CENPJ | ENST00000616936.4 | c.*358A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 15/16 | 1 | ||||
CENPJ | ENST00000545981.6 | c.*444A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 17/18 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at