rs79290524
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP3_ModerateBP6
The NM_006612.6(KIF1C):āc.1136C>Gā(p.Ala379Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000499 in 1,614,240 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.00032 ( 0 hom., cov: 32)
Exomes š: 0.00052 ( 1 hom. )
Consequence
KIF1C
NM_006612.6 missense
NM_006612.6 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 4.95
Genes affected
KIF1C (HGNC:6317): (kinesin family member 1C) The protein encoded by this gene is a member of the kinesin-like protein family. The family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. Mutations in this gene are a cause of spastic ataxia 2, autosomal recessive. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BP6
?
Variant 17-5004971-C-G is Benign according to our data. Variant chr17-5004971-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 468849.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=2, Likely_benign=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF1C | NM_006612.6 | c.1136C>G | p.Ala379Gly | missense_variant | 13/23 | ENST00000320785.10 | |
KIF1C | XM_005256424.3 | c.1136C>G | p.Ala379Gly | missense_variant | 14/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF1C | ENST00000320785.10 | c.1136C>G | p.Ala379Gly | missense_variant | 13/23 | 1 | NM_006612.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152244Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000422 AC: 106AN: 251392Hom.: 1 AF XY: 0.000456 AC XY: 62AN XY: 135876
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GnomAD4 exome AF: 0.000518 AC: 757AN: 1461878Hom.: 1 Cov.: 32 AF XY: 0.000534 AC XY: 388AN XY: 727240
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GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74510
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Hereditary spastic paraplegia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Nov 01, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | KIF1C: PP3 - |
Spastic ataxia 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
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DS_DL_spliceai
Position offset: 29
Find out detailed SpliceAI scores and Pangolin per-transcript scores at