rs143314146

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001130100.2(KIFC3):​c.1906G>C​(p.Glu636Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. E636K) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

KIFC3
NM_001130100.2 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.06
Variant links:
Genes affected
KIFC3 (HGNC:6326): (kinesin family member C3) This gene encodes a member of the kinesin-14 family of microtubule motors. Members of this family play a role in the formation, maintenance and remodeling of the bipolar mitotic spindle. The protein encoded by this gene has cytoplasmic functions in the interphase cells. It may also be involved in the final stages of cytokinesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

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 rank MANE Protein UniProt
KIFC3NM_001130100.2 linkc.1906G>C p.Glu636Gln missense_variant Exon 15 of 20 ENST00000445690.7 NP_001123572.1 Q9BVG8-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIFC3ENST00000445690.7 linkc.1906G>C p.Glu636Gln missense_variant Exon 15 of 20 1 NM_001130100.2 ENSP00000401696.2 Q9BVG8-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461696
Hom.:
0
Cov.:
35
AF XY:
0.00000275
AC XY:
2
AN XY:
727158
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
0.0019
T
BayesDel_noAF
Benign
-0.24
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.19
.;T;.;.;.;.;T;.;.
Eigen
Benign
0.076
Eigen_PC
Benign
0.13
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Uncertain
0.94
.;D;D;.;D;D;D;D;D
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.44
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.95
.;L;L;.;.;.;.;.;.
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-0.66
N;N;N;N;N;N;N;N;N
REVEL
Benign
0.22
Sift
Benign
0.14
T;T;T;T;T;T;T;T;D
Sift4G
Benign
0.34
T;T;T;T;T;T;T;T;T
Polyphen
0.73, 0.56
.;P;.;.;.;P;P;.;.
Vest4
0.46
MutPred
0.68
.;.;.;.;Loss of disorder (P = 0.0974);.;.;.;.;
MVP
0.78
MPC
1.2
ClinPred
0.58
D
GERP RS
5.1
Varity_R
0.24
gMVP
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-57795050; API