chr6-17794263-G-C

Position:

• chr6-17794263-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_022113.6(KIF13A):​c.3208C>G​(p.Leu1070Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: KIF13A NM_022113.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.30621287).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF13A	NM_022113.6	c.3208C>G	p.Leu1070Val	missense_variant	25/39	ENST00000259711.11	NP_071396.4
KIF13A	NM_001105566.3	c.3208C>G	p.Leu1070Val	missense_variant	25/38		NP_001099036.1
KIF13A	NM_001105567.3	c.3208C>G	p.Leu1070Val	missense_variant	25/37		NP_001099037.1
KIF13A	NM_001105568.4	c.3208C>G	p.Leu1070Val	missense_variant	25/38		NP_001099038.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF13A	ENST00000259711.11	c.3208C>G	p.Leu1070Val	missense_variant	25/39	1	NM_022113.6	ENSP00000259711

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.53
BayesDel_addAF	Uncertain	0.082	D
BayesDel_noAF	Benign	-0.12
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.044	.;T;T;.;.;T
Eigen	Uncertain	0.23
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	D;T;D;D;D;D
M_CAP	Benign	0.029	D
MetaRNN	Benign	0.31	T;T;T;T;T;T
MetaSVM	Benign	-0.49	T
MutationAssessor	Uncertain	2.1	M;.;M;M;M;.
MutationTaster	Benign	0.97	P;P;P;P;P;P
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-1.7	N;N;N;N;N;.
REVEL	Benign	0.20
Sift	Benign	0.14	T;T;D;T;T;.
Sift4G	Benign	0.23	T;D;T;T;T;.
Polyphen		0.72	P;.;B;P;D;.
Vest4		0.55
MutPred		0.19		Gain of MoRF binding (P = 0.0857);.;Gain of MoRF binding (P = 0.0857);Gain of MoRF binding (P = 0.0857);Gain of MoRF binding (P = 0.0857);.;
MVP		0.59
MPC		0.88
ClinPred		0.86	D
GERP RS		3.6
Varity_R		0.13
gMVP		0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734234; hg19: chr6-17794494;