KIF12

kinesin family member 12, the group of Kinesins

Basic information

Region (hg38): 9:114086126-114099292

Links

ENSG00000136883

∙ NCBI:113220 ∙ OMIM:611278 ∙ HGNC:21495 ∙ Uniprot:Q96FN5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

cholestasis (Definitive), mode of inheritance: AR
cholestasis, progressive familial intrahepatic, 8 (Strong), mode of inheritance: AR
cholestasis, progressive familial intrahepatic, 8 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cholestasis, progressive familial intrahepatic, 8	AR	Gastrointestinal	Medical management may be beneficial as pertains to cholestasis and related sequelae; Liver transplant has been described	Gastrointestinal	30250217; 30976738; 34555379

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF12 gene.

Inborn_genetic_diseases (91 variants)
not_provided (55 variants)
Cholestasis,_progressive_familial_intrahepatic,_8 (11 variants)
KIF12-related_disorder (3 variants)
Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001388308.1. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	8 clinvar	4 clinvar	13
missense		2 clinvar	92 clinvar	10 clinvar	6 clinvar	110
nonsense	3 clinvar	1 clinvar	1 clinvar			5
start loss						0
frameshift	1 clinvar	1 clinvar	1 clinvar			3
splice donor/acceptor (+/-2bp)		2 clinvar				2
Total	4	6	95	18	10

Highest pathogenic variant AF is 0.000026256072

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF12	protein_coding	protein_coding	ENST00000374118	14	13102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.16e-12	0.763	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.656	276	308	0.895	0.0000185	3228
Missense in Polyphen		78	93.933	0.83038		1033
Synonymous	0.343	115	120	0.960	0.00000613	1095
Loss of Function	1.70	23	33.6	0.684	0.00000217	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000421
Ashkenazi Jewish	0.000109	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000193	0.000185
European (Non-Finnish)	0.000188	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000990	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.0995

Intolerance Scores

loftool: 0.616
rvis_EVS: -0.13
rvis_percentile_EVS: 43.98

Haploinsufficiency Scores

pHI: 0.0657
hipred: N
hipred_score: 0.435
ghis: 0.440

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Kif12
Phenotype

Gene ontology

Biological process: microtubule-based movement;biological_process
Cellular component: cytoplasm;kinesin complex;microtubule;extracellular exosome
Molecular function: molecular_function;microtubule motor activity;ATP binding;microtubule binding;ATPase activity