KIF12
Basic information
Region (hg38): 9:114086126-114099292
Links
Phenotypes
GenCC
Source:
- cholestasis (Definitive), mode of inheritance: AR
- cholestasis, progressive familial intrahepatic, 8 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
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
- not provided (2 variants)
- Cholestasis, progressive familial intrahepatic, 8 (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 | 13 | |||||
missense | 42 | 54 | ||||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 3 | 1 | 5 | ||
non coding | 11 | |||||
Total | 3 | 5 | 44 | 19 | 15 |
Highest pathogenic variant AF is 0.0000131
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) | ||
9-114092411-T-A | KIF12-related disorder | Uncertain significance (Aug 23, 2024) | ||
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) |
GnomAD
Source:
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:
- 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