KIF13A

kinesin family member 13A, the group of Kinesins

Basic information

Region (hg38): 6:17759183-17987635

Links

ENSG00000137177 ∙ NCBI:63971 ∙ OMIM:605433 ∙ HGNC:14566 ∙ Uniprot:Q9H1H9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF13A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF13A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	4	6
missense			75	2	3	80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	75	4	7

Variants in KIF13A

This is a list of pathogenic ClinVar variants found in the KIF13A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-17764136-C-T		not specified	Uncertain significance (Jul 14, 2024)
6-17764153-A-G		not specified	Uncertain significance (Jan 31, 2024)
6-17764169-A-C		not specified	Uncertain significance (Aug 05, 2024)
6-17764189-G-A		not specified	Uncertain significance (Aug 04, 2021)
6-17764207-G-A		not specified	Uncertain significance (Apr 18, 2023)
6-17764223-C-T		not specified	Uncertain significance (Jun 04, 2024)
6-17764234-G-A		not specified	Uncertain significance (Jul 22, 2024)
6-17764257-C-G		not specified	Uncertain significance (Jan 06, 2023)
6-17764277-T-C		not specified	Uncertain significance (Feb 28, 2024)
6-17764346-T-C		not specified	Uncertain significance (Mar 01, 2024)
6-17764348-G-A		not specified	Uncertain significance (Jan 17, 2024)
6-17764363-G-T		not specified	Uncertain significance (Mar 18, 2024)
6-17764398-G-C		not specified	Uncertain significance (Mar 28, 2024)
6-17764555-C-G		not specified	Uncertain significance (Jun 23, 2021)
6-17764562-C-T			Likely benign (Apr 01, 2023)
6-17764579-T-G		not specified	Uncertain significance (Oct 03, 2023)
6-17764603-T-G		not specified	Uncertain significance (Dec 03, 2024)
6-17764647-C-T			Likely benign (Apr 01, 2022)
6-17764665-G-C			Benign (Aug 15, 2018)
6-17764735-C-T		not specified	Uncertain significance (Dec 08, 2023)
6-17764765-C-T		not specified	Uncertain significance (Dec 02, 2022)
6-17764819-A-G		not specified	Uncertain significance (Nov 10, 2024)
6-17764846-T-C		not specified	Uncertain significance (Apr 08, 2024)
6-17764871-C-G		not specified	Uncertain significance (Apr 17, 2023)
6-17764906-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF13A	protein_coding	protein_coding	ENST00000259711	39	228441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000622	124604	0	50	124654	0.000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	774	952	0.813	0.0000509	11809
Missense in Polyphen		301	428.87	0.70185		5305
Synonymous	0.308	354	361	0.979	0.0000202	3426
Loss of Function	7.86	15	99.7	0.150	0.00000592	1131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000503	0.000499
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000391	0.000389
Finnish	0.0000948	0.0000928
European (Non-Finnish)	0.000197	0.000195
Middle Eastern	0.000391	0.000389
South Asian	0.000241	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plus end-directed microtubule-dependent motor protein involved in intracellular transport and regulating various processes such as mannose-6-phosphate receptor (M6PR) transport to the plasma membrane, endosomal sorting during melanosome biogenesis and cytokinesis. Mediates the transport of M6PR- containing vesicles from trans-Golgi network to the plasma membrane via direct interaction with the AP-1 complex. During melanosome maturation, required for delivering melanogenic enzymes from recycling endosomes to nascent melanosomes by creating peripheral recycling endosomal subdomains in melanocytes. Also required for the abcission step in cytokinesis: mediates translocation of ZFYVE26, and possibly TTC19, to the midbody during cytokinesis. {ECO:0000269|PubMed:19841138, ECO:0000269|PubMed:20208530}.
• Pathway: Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Protein folding (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.554
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.5

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.603
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.681

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kif13a
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: intracellular protein transport;microtubule-based movement;cell cycle;endosome to lysosome transport;melanosome organization;regulation of cytokinesis;vesicle cargo loading;Golgi to plasma membrane protein transport;cell division;plus-end-directed vesicle transport along microtubule
• Cellular component: centrosome;kinesin complex;microtubule;endosome membrane;midbody;trans-Golgi network membrane
• Molecular function: microtubule motor activity;protein binding;ATP binding;microtubule binding;ATPase activity