KIF13A p.Leu1070Leu

Variant names:

• chr6-17794260-C-C
• NM_022113.6:c.

Your query was ambiguous. Multiple possible variants found:

• chr6-17794261--
• chr6-17794263-G-A
• chr6-17794261-C-A
• chr6-17794261-C-G
• chr6-17794261-C-T
• chr6-17794261-CAG-TAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_022113.6(KIF13A):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KIF13A NM_022113.6 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022113.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13A	NM_022113.6	MANE Select	c.		exon_region	Exon 25 of 39	NP_071396.4
	KIF13A	NM_001105566.3		c.		exon_region	Exon 25 of 38	NP_001099036.1	Q9H1H9-2
	KIF13A	NM_001105567.3		c.		exon_region	Exon 25 of 37	NP_001099037.1	Q9H1H9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13A	ENST00000259711.11	TSL:1 MANE Select	c.		exon_region	Exon 25 of 39	ENSP00000259711.6	Q9H1H9-1
	KIF13A	ENST00000378826.6	TSL:1	c.		exon_region	Exon 25 of 38	ENSP00000368103.2	Q9H1H9-2
	KIF13A	ENST00000378843.6	TSL:1	c.		exon_region	Exon 25 of 37	ENSP00000368120.2	Q9H1H9-4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-17794491;