KIFAP3

kinesin associated protein 3, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 1:169921326-170085208

Links

ENSG00000075945 ∙ NCBI:22920 ∙ OMIM:601836 ∙ HGNC:17060 ∙ Uniprot:Q92845 ∙ 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 KIFAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIFAP3 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				1	2	3
missense			20		2	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	20	3	4

Variants in KIFAP3

This is a list of pathogenic ClinVar variants found in the KIFAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-169921722-T-G		not specified	Uncertain significance (Nov 01, 2021)
1-169921738-G-T		not specified	Uncertain significance (Mar 30, 2024)
1-169954029-T-C		not specified	Uncertain significance (Apr 08, 2022)
1-169954070-G-T		not specified	Uncertain significance (Jul 25, 2023)
1-169954083-A-G		not specified	Uncertain significance (Jan 23, 2023)
1-169961094-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-169978103-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-169981976-T-C		KIFAP3-related disorder	Likely benign (Sep 02, 2020)
1-169982043-G-C		not specified	Uncertain significance (May 02, 2024)
1-169982779-G-T		not specified	Uncertain significance (Apr 28, 2023)
1-169982825-C-T		not specified	Uncertain significance (Aug 10, 2021)
1-169982837-A-C		KIFAP3-related disorder	Benign (Dec 23, 2019)
1-169984604-T-G		not specified	Uncertain significance (Mar 21, 2023)
1-169984674-A-C		KIFAP3-related disorder	Benign (Jul 26, 2019)
1-169992194-G-A		KIFAP3-related disorder	Benign (Jul 10, 2019)
1-169992204-A-C		not specified	Uncertain significance (Dec 20, 2021)
1-170016518-C-T		not specified	Uncertain significance (Sep 15, 2021)
1-170016525-C-G		not specified	Uncertain significance (Feb 28, 2024)
1-170024507-C-T		not specified	Uncertain significance (Feb 23, 2023)
1-170024563-T-C		not specified	Uncertain significance (Feb 17, 2024)
1-170031893-T-C		KIFAP3-related disorder	Benign (May 30, 2019)
1-170034440-T-C		not specified	Uncertain significance (Jun 05, 2024)
1-170039253-G-A		not specified	Uncertain significance (Dec 13, 2023)
1-170041738-A-G		KIFAP3-related disorder	Likely benign (Aug 13, 2019)
1-170041756-C-T		KIFAP3-related disorder	Likely benign (Feb 26, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIFAP3	protein_coding	protein_coding	ENST00000361580	20	163883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000158	1.00	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	295	403	0.732	0.0000197	5248
Missense in Polyphen		79	145.19	0.54413		1995
Synonymous	-0.862	149	136	1.09	0.00000633	1393
Loss of Function	4.05	17	47.0	0.362	0.00000283	557

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000313	0.000309
Ashkenazi Jewish	0.000212	0.000198
East Asian	0.0000546	0.0000544
Finnish	0.000478	0.000462
European (Non-Finnish)	0.000207	0.000193
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000329	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in tethering the chromosomes to the spindle pole and in chromosome movement. Binds to the tail domain of the KIF3A/KIF3B heterodimer to form a heterotrimeric KIF3 complex and may regulate the membrane binding of this complex (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Translocation of GLUT4 to the plasma membrane;Intra-Golgi and retrograde Golgi-to-ER traffic;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• loftool: 0.736
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.324
• hipred: N
• hipred_score: 0.499
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kifap3
• Phenotype: muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; embryo phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based process;microtubule-based movement;signal transduction;negative regulation of cell population proliferation;antigen processing and presentation of exogenous peptide antigen via MHC class II;intraciliary transport involved in cilium assembly;negative regulation of apoptotic process;positive regulation of calcium-dependent cell-cell adhesion;protein-containing complex assembly;plus-end-directed vesicle transport along microtubule
• Cellular component: condensed nuclear chromosome;endoplasmic reticulum;Golgi apparatus;centrosome;cytosol;spindle microtubule;cilium;axoneme;microtubule cytoskeleton;kinesin II complex;photoreceptor connecting cilium;ciliary basal body;ciliary tip;periciliary membrane compartment
• Molecular function: protein binding;kinesin binding;protein phosphatase binding;intraciliary transport particle B binding