rs201684653
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP2BP4_ModerateBP6
The NM_001244008.2(KIF1A):c.3886C>T(p.Arg1296Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,586,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1296G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001244008.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1A | NM_001244008.2 | c.3886C>T | p.Arg1296Cys | missense_variant | 37/49 | ENST00000498729.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1A | ENST00000498729.9 | c.3886C>T | p.Arg1296Cys | missense_variant | 37/49 | 5 | NM_001244008.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000288 AC: 6AN: 208122Hom.: 0 AF XY: 0.00000893 AC XY: 1AN XY: 112012
GnomAD4 exome AF: 0.00000906 AC: 13AN: 1434592Hom.: 0 Cov.: 32 AF XY: 0.00000844 AC XY: 6AN XY: 710914
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74472
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2019 | The p.R1195C variant (also known as c.3583C>T), located in coding exon 34 of the KIF1A gene, results from a C to T substitution at nucleotide position 3583. The arginine at codon 1195 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Neuropathy, hereditary sensory, type 2C;C5235139:Hereditary spastic paraplegia 30;C5393830:Intellectual disability, autosomal dominant 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at