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.

• not_specified (65 variants)
• KIFAP3-related_disorder (7 variants)

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. These statistics are base on transcript: NM_000014970.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	1	2	5
missense			70	1	2	73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	74	2	4

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
		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

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

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