rs587777033
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_001098511.3(KIF2A):c.961C>G(p.His321Asp) 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. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H321P) has been classified as Pathogenic.
Frequency
Consequence
NM_001098511.3 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF2A | NM_001098511.3 | c.961C>G | p.His321Asp | missense_variant, splice_region_variant | 10/21 | ENST00000407818.8 | |
KIF2A | NM_004520.5 | c.961C>G | p.His321Asp | missense_variant, splice_region_variant | 10/20 | ||
KIF2A | NM_001243953.2 | c.904C>G | p.His302Asp | missense_variant, splice_region_variant | 10/20 | ||
KIF2A | NM_001243952.2 | c.880C>G | p.His294Asp | missense_variant, splice_region_variant | 11/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF2A | ENST00000407818.8 | c.961C>G | p.His321Asp | missense_variant, splice_region_variant | 10/21 | 1 | NM_001098511.3 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 26
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Complex cortical dysplasia with other brain malformations 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at