6-17764735-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022113.6(KIF13A):c.4793G>A(p.Gly1598Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Consequence
KIF13A
NM_022113.6 missense
NM_022113.6 missense
Scores
8
6
5
Clinical Significance
Conservation
PhyloP100: 7.57
Genes affected
KIF13A (HGNC:14566): (kinesin family member 13A) This gene encodes a member of the kinesin family of microtubule-based motor proteins that function in the positioning of endosomes. This family member can direct mannose-6-phosphate receptor-containing vesicles from the trans-Golgi network to the plasma membrane, and it is necessary for the steady-state distribution of late endosomes/lysosomes. It is also required for the translocation of FYVE-CENT and TTC19 from the centrosome to the midbody during cytokinesis, and it plays a role in melanosome maturation. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIF13A | NM_022113.6 | c.4793G>A | p.Gly1598Asp | missense_variant | 39/39 | ENST00000259711.11 | NP_071396.4 | |
KIF13A | NM_001105566.3 | c.4688G>A | p.Gly1563Asp | missense_variant | 38/38 | NP_001099036.1 | ||
KIF13A | NM_001105567.3 | c.4649G>A | p.Gly1550Asp | missense_variant | 37/37 | NP_001099037.1 | ||
KIF13A | NM_001105568.4 | c.4649G>A | p.Gly1550Asp | missense_variant | 37/38 | NP_001099038.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIF13A | ENST00000259711.11 | c.4793G>A | p.Gly1598Asp | missense_variant | 39/39 | 1 | NM_022113.6 | ENSP00000259711.6 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247140Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134036
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74258
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.4793G>A (p.G1598D) alteration is located in exon 39 (coding exon 39) of the KIF13A gene. This alteration results from a G to A substitution at nucleotide position 4793, causing the glycine (G) at amino acid position 1598 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T;T;.;.;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L;.;.;.
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D;D;.
REVEL
Uncertain
Sift
Pathogenic
D;D;D;D;D;.
Sift4G
Pathogenic
D;D;D;D;D;.
Polyphen
D;.;D;D;D;.
Vest4
MutPred
0.41
.;.;Gain of helix (P = 0.0496);.;.;.;
MVP
MPC
1.0
ClinPred
D
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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at