KIF12

kinesin family member 12, the group of Kinesins

Basic information

Region (hg38): 9:114086125-114099292

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

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.

• not provided (34 variants)
• Inborn genetic diseases (24 variants)
• Cholestasis, progressive familial intrahepatic, 8 (4 variants)
• KIF12-related condition (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.

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				4	4	8
missense		1	26	4	7	38
nonsense	1					1
start loss						0
frameshift		1	1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding			1	3	3	7
Total	1	2	28	11	14

Highest pathogenic variant AF is 0.0000460

Variants in KIF12

This is a list of pathogenic ClinVar variants found in the KIF12 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-114091869-G-C			Benign (Oct 05, 2023)
9-114091896-C-T			Benign (Nov 27, 2023)
9-114091903-A-C		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 16, 2023)
9-114091903-A-G			Benign (Jan 25, 2024)
9-114091916-TG-T			Uncertain significance (May 15, 2022)
9-114091922-C-T		Inborn genetic diseases	Uncertain significance (Aug 23, 2021)
9-114091931-C-T		Inborn genetic diseases	Uncertain significance (Aug 04, 2022)
9-114091975-G-A			Likely benign (May 21, 2022)
9-114091992-C-T			Uncertain significance (Jul 02, 2022)
9-114091998-C-T		Inborn genetic diseases	Uncertain significance (Jun 27, 2023)
9-114092347-G-A		Inborn genetic diseases	Uncertain significance (Apr 22, 2022)
9-114092378-G-C		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
9-114092409-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 14, 2023)
9-114092425-C-T		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
9-114092426-G-A		Cholestasis, progressive familial intrahepatic, 8	Likely pathogenic (Mar 25, 2024)
9-114092434-G-C			Conflicting classifications of pathogenicity (Oct 20, 2023)
9-114092438-A-T		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
9-114092452-C-G			Likely pathogenic (Oct 22, 2022)
9-114092455-G-T		Malignant tumor of prostate	Uncertain significance (-)
9-114092556-C-T			Likely benign (Dec 14, 2023)
9-114092574-G-A			Benign (Dec 26, 2023)
9-114092579-G-A		Inborn genetic diseases	Uncertain significance (Feb 17, 2023)
9-114093215-A-G			Likely benign (Dec 04, 2023)
9-114093229-C-T			Uncertain significance (Aug 30, 2022)
9-114093264-A-C		Inborn genetic diseases	Uncertain significance (Apr 27, 2022)

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

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