KLC4
Basic information
Region (hg38): 6:43040777-43075095
Previous symbols: [ "KNSL8" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLC4 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 | 0 | |||||
missense | 48 | 48 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 3 | |||||
Total | 0 | 1 | 50 | 0 | 1 |
Variants in KLC4
This is a list of pathogenic ClinVar variants found in the KLC4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-43040904-T-C | Likely benign (Jun 03, 2024) | |||
6-43040924-T-C | Inborn genetic diseases | Uncertain significance (Oct 14, 2023) | ||
6-43040942-A-G | Inborn genetic diseases | Uncertain significance (Jul 11, 2023) | ||
6-43040952-C-T | Inborn genetic diseases | Uncertain significance (Nov 30, 2024) | ||
6-43040953-G-A | CUL7-related disorder | Benign (Aug 12, 2024) | ||
6-43040956-G-A | Likely benign (Dec 30, 2021) | |||
6-43040959-AATCAGGACAGCT-GC | Pathogenic (Nov 30, 2019) | |||
6-43040962-C-T | Likely benign (Oct 22, 2024) | |||
6-43040965-G-A | Likely benign (Dec 21, 2020) | |||
6-43040971-T-TTGCAGGCATTGCTGCAGCTGTGCCAGCC | 3M syndrome 1 | Likely pathogenic (-) | ||
6-43040974-C-T | 3M syndrome 1 • CUL7-related disorder | Conflicting classifications of pathogenicity (Aug 02, 2024) | ||
6-43040999-C-T | Inborn genetic diseases | Uncertain significance (Oct 29, 2024) | ||
6-43041005-A-G | Inborn genetic diseases | Uncertain significance (Aug 05, 2024) | ||
6-43041015-C-A | Inborn genetic diseases | Uncertain significance (Oct 17, 2023) | ||
6-43041026-C-T | not specified • 3M syndrome 1 • CUL7-related disorder | Benign/Likely benign (Jan 15, 2025) | ||
6-43041036-G-A | 3M syndrome 1 | Likely pathogenic (Oct 10, 2014) | ||
6-43041056-C-T | Uncertain significance (Dec 20, 2021) | |||
6-43041058-G-A | Likely benign (Dec 17, 2024) | |||
6-43041076-C-A | 3M syndrome 1 | Likely pathogenic (Jun 04, 2024) | ||
6-43041086-G-A | Likely benign (Sep 10, 2023) | |||
6-43041089-G-A | not specified | Likely benign (Apr 23, 2025) | ||
6-43041138-A-G | Benign (Nov 12, 2018) | |||
6-43042768-G-T | CUL7-related disorder | Likely benign (Apr 30, 2019) | ||
6-43042795-G-A | Likely benign (Mar 13, 2022) | |||
6-43042799-T-C | Uncertain significance (Jan 17, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KLC4 | protein_coding | protein_coding | ENST00000259708 | 16 | 34323 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00119 | 0.999 | 125674 | 0 | 74 | 125748 | 0.000294 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.893 | 340 | 390 | 0.873 | 0.0000239 | 4100 |
Missense in Polyphen | 127 | 146.6 | 0.86628 | 1613 | ||
Synonymous | 1.54 | 128 | 152 | 0.842 | 0.00000794 | 1301 |
Loss of Function | 3.75 | 12 | 36.5 | 0.329 | 0.00000179 | 410 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000177 | 0.000177 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000381 | 0.000381 |
Finnish | 0.000185 | 0.000185 |
European (Non-Finnish) | 0.000397 | 0.000396 |
Middle Eastern | 0.000381 | 0.000381 |
South Asian | 0.000294 | 0.000294 |
Other | 0.000653 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity (By similarity). {ECO:0000250}.;
- Pathway
- Salmonella infection - Homo sapiens (human);Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;RHO GTPases activate KTN1;Kinesins;Factors involved in megakaryocyte development and platelet production;RHO GTPase Effectors;Signaling by Rho GTPases;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
- 0.104
Intolerance Scores
- loftool
- 0.477
- rvis_EVS
- -0.26
- rvis_percentile_EVS
- 34.93
Haploinsufficiency Scores
- pHI
- 0.286
- hipred
- N
- hipred_score
- 0.385
- ghis
- 0.529
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.940
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Klc4
- Phenotype
Gene ontology
- Biological process
- Cellular component
- cytoplasm;kinesin complex;microtubule
- Molecular function
- microtubule motor activity;protein binding