KLC4
gene geneOn this page
Also known as bA387M24.3
Summary
KLC4 (kinesin light chain 4, HGNC:21624) is a protein-coding gene on chromosome 6p21.1, encoding Kinesin light chain 4 (Q9NSK0). Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport.
Predicted to enable kinesin binding activity. Predicted to be involved in microtubule-based movement. Predicted to be located in microtubule. Predicted to be part of kinesin complex. Predicted to be active in cytoplasm.
Source: NCBI Gene 89953 — RefSeq curated summary.
At a glance
- Gene–disease (curated): early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy (Limited, GenCC)
- GWAS associations: 1
- Clinical variants (ClinVar): 120 total — 1 pathogenic, 1 likely-pathogenic
- Phenotypes (HPO): 31
- MANE Select transcript:
NM_201521
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:21624 |
| Approved symbol | KLC4 |
| Name | kinesin light chain 4 |
| Location | 6p21.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | bA387M24.3 |
| Ensembl gene | ENSG00000137171 |
| Ensembl biotype | protein_coding |
| OMIM | 620909 |
| Entrez | 89953 |
Gene structure
Transcript identifiers
Ensembl transcripts: 50 — 42 protein_coding, 5 retained_intron, 3 nonsense_mediated_decay
ENST00000259708, ENST00000347162, ENST00000394056, ENST00000453940, ENST00000458460, ENST00000460283, ENST00000463063, ENST00000463168, ENST00000467906, ENST00000468114, ENST00000469987, ENST00000470728, ENST00000472172, ENST00000472792, ENST00000479388, ENST00000479632, ENST00000481499, ENST00000481888, ENST00000486439, ENST00000905002, ENST00000905003, ENST00000905004, ENST00000905005, ENST00000905006, ENST00000905007, ENST00000905008, ENST00000905009, ENST00000905010, ENST00000905011, ENST00000905012, ENST00000905013, ENST00000905014, ENST00000905015, ENST00000905016, ENST00000905017, ENST00000905018, ENST00000928701, ENST00000928702, ENST00000928703, ENST00000928704, ENST00000928705, ENST00000945947, ENST00000945948, ENST00000945949, ENST00000945950, ENST00000945951, ENST00000945952, ENST00000945953, ENST00000945954, ENST00000945955
RefSeq mRNA: 6 — MANE Select: NM_201521
NM_001289034, NM_001289035, NM_138343, NM_201521, NM_201522, NM_201523
CCDS: CCDS47429, CCDS4882, CCDS4883, CCDS75459
Canonical transcript exons
ENST00000347162 — 16 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001857391 | 43074622 | 43075093 |
| ENSE00001861736 | 43059631 | 43059685 |
| ENSE00003469526 | 43070692 | 43070865 |
| ENSE00003476023 | 43071275 | 43071374 |
| ENSE00003488048 | 43073223 | 43073338 |
| ENSE00003498980 | 43066306 | 43066525 |
| ENSE00003519174 | 43062917 | 43063147 |
| ENSE00003519580 | 43072147 | 43072255 |
| ENSE00003539457 | 43061311 | 43061593 |
| ENSE00003541538 | 43071567 | 43071619 |
| ENSE00003556776 | 43073902 | 43073965 |
| ENSE00003581670 | 43065620 | 43065701 |
| ENSE00003633101 | 43072824 | 43072964 |
| ENSE00003645370 | 43071852 | 43071922 |
| ENSE00003667895 | 43070354 | 43070455 |
| ENSE00003789566 | 43066996 | 43067083 |
Expression profiles
Bgee: expression breadth ubiquitous, 240 present calls, max score 97.56.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9393 / max 99.0182, expressed in 1723 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 67855 | 5.3853 | 1656 |
| 203996 | 0.8258 | 519 |
| 67857 | 0.4134 | 72 |
| 67856 | 0.2721 | 126 |
| 203997 | 0.0428 | 19 |
Top tissues by expression
255 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right lobe of liver | UBERON:0001114 | 97.56 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 97.02 | gold quality |
| right hemisphere of cerebellum | UBERON:0014890 | 95.96 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 95.93 | gold quality |
| cerebellar cortex | UBERON:0002129 | 95.83 | gold quality |
| transverse colon | UBERON:0001157 | 95.14 | gold quality |
| ileal mucosa | UBERON:0000331 | 95.03 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 94.91 | gold quality |
| cerebellum | UBERON:0002037 | 94.75 | gold quality |
| apex of heart | UBERON:0002098 | 94.51 | gold quality |
| small intestine | UBERON:0002108 | 94.09 | gold quality |
| rectum | UBERON:0001052 | 94.06 | gold quality |
| liver | UBERON:0002107 | 93.94 | gold quality |
| right uterine tube | UBERON:0001302 | 93.75 | gold quality |
| pituitary gland | UBERON:0000007 | 93.73 | gold quality |
| adenohypophysis | UBERON:0002196 | 93.55 | gold quality |
| metanephros cortex | UBERON:0010533 | 93.55 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 93.43 | gold quality |
| pancreatic ductal cell | CL:0002079 | 93.29 | silver quality |
| right frontal lobe | UBERON:0002810 | 93.07 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 92.94 | gold quality |
| kidney epithelium | UBERON:0004819 | 92.77 | gold quality |
| cardiac muscle of right atrium | UBERON:0003379 | 92.74 | silver quality |
| left ovary | UBERON:0002119 | 92.57 | gold quality |
| body of stomach | UBERON:0001161 | 92.35 | gold quality |
| intestine | UBERON:0000160 | 92.27 | gold quality |
| cortex of kidney | UBERON:0001225 | 92.15 | gold quality |
| left testis | UBERON:0004533 | 92.13 | gold quality |
| thyroid gland | UBERON:0002046 | 92.07 | gold quality |
| right testis | UBERON:0004534 | 92.01 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.77 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
19 targeting KLC4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-5680 | 99.91 | 69.83 | 3421 |
| HSA-MIR-3919 | 99.87 | 69.45 | 2489 |
| HSA-MIR-3065-3P | 99.87 | 70.25 | 1407 |
| HSA-MIR-498-5P | 99.76 | 69.64 | 1807 |
| HSA-MIR-580-3P | 99.67 | 69.23 | 1841 |
| HSA-MIR-578 | 99.46 | 68.36 | 1787 |
| HSA-MIR-4436B-3P | 98.25 | 65.26 | 1494 |
| HSA-MIR-6735-5P | 98.24 | 65.36 | 1488 |
| HSA-MIR-7843-5P | 98.12 | 65.26 | 1421 |
| HSA-MIR-4632-5P | 97.82 | 65.38 | 1470 |
| HSA-MIR-6879-5P | 97.77 | 65.52 | 1521 |
| HSA-MIR-3116 | 97.07 | 65.78 | 1324 |
| HSA-MIR-3674 | 97.01 | 68.86 | 1171 |
| HSA-MIR-3616-3P | 96.96 | 65.45 | 983 |
| HSA-MIR-4491 | 96.53 | 66.20 | 935 |
| HSA-MIR-4657 | 96.53 | 66.57 | 895 |
| HSA-MIR-1226-5P | 96.50 | 65.28 | 643 |
| HSA-MIR-3174 | 94.63 | 63.64 | 577 |
Literature-anchored findings (GeneRIF, showing 4)
- Data reveal aspects of the molecular mechanism of kinesin-8 motors that contribute to their unique dual motile and depolymerising functions, which are adapted to control microtubule length. (PMID:20818331)
- The association of a KLC4 mutation with spastic paraplegia identifies a new locus for the disease. (PMID:26423925)
- Findings indicate that SET domain protein 3 (SETD3) down-regulated the expression of kinesin light chain 4 (KLC4), contributing to the radiosensitivity of cervical cancer cells, suggesting targeting SETD3 might be a potential strategy for the clinical management of cervical cancer. (PMID:31235251)
- Kinesin light chain 4 as a new target for lung cancer chemoresistance via targeted inhibition of checkpoint kinases in the DNA repair network. (PMID:32457423)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | klc3 | ENSDARG00000055965 |
| danio_rerio | klc4 | ENSDARG00000086985 |
| mus_musculus | Klc4 | ENSMUSG00000003546 |
| rattus_norvegicus | Klc4 | ENSRNOG00000018168 |
Paralogs (5): APPBP2 (ENSG00000062725), KLC3 (ENSG00000104892), NPHP3 (ENSG00000113971), KLC1 (ENSG00000126214), KLC2 (ENSG00000174996)
Protein
Protein identifiers
Kinesin light chain 4 — Q9NSK0 (reviewed: Q9NSK0)
Alternative names: Kinesin-like protein 8
All UniProt accessions (8): C9J8T5, C9JQU1, C9JXT5, C9JZE5, C9K0D5, Q9NSK0, F8WCA4, H7C4M1
UniProt curated annotations — full annotation on UniProt →
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.
Subunit / interactions. Oligomeric complex composed of two heavy chains and two light chains.
Subcellular location. Cytoplasm. Cytoskeleton.
Disease relevance. Neurodegeneration, early-childhood-onset, with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy (CONDRHN) [MIM:621129] An autosomal recessive, early-onset neurodegenerative disorder characterized by progressive walking difficulties with spasticity or ataxia resulting in loss of ambulation, retinitis pigmentosa causing progressive visual impairment and blindness, sensorineural hearing loss, demyelinating peripheral neuropathy, and severely impaired intellectual development with poor or absent speech. The disease may be caused by variants affecting the gene represented in this entry.
Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.
Similarity. Belongs to the kinesin light chain family.
Isoforms (5)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9NSK0-1 | 1 | yes |
| Q9NSK0-2 | 2 | |
| Q9NSK0-3 | 3 | |
| Q9NSK0-4 | 4 | |
| Q9NSK0-5 | 5 |
RefSeq proteins (6): NP_001275963, NP_001275964, NP_612352, NP_958929, NP_958930, NP_958931 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002151 | Kinesin_light | Family |
| IPR011990 | TPR-like_helical_dom_sf | Homologous_superfamily |
| IPR015792 | Kinesin_light_repeat | Repeat |
| IPR019734 | TPR_rpt | Repeat |
Pfam: PF13374, PF13424
UniProt features (34 total): modified residue 8, repeat 7, splice variant 6, sequence conflict 4, region of interest 3, compositionally biased region 2, initiator methionine 1, chain 1, coiled-coil region 1, sequence variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NSK0-F1 | 72.78 | 0.43 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (8): 2, 174, 460, 519, 565, 566, 590, 612
Function
Pathways and Gene Ontology
Reactome pathways
16 pathways
| ID | Pathway |
|---|---|
| R-HSA-2132295 | MHC class II antigen presentation |
| R-HSA-5625970 | RHO GTPases activate KTN1 |
| R-HSA-6811434 | COPI-dependent Golgi-to-ER retrograde traffic |
| R-HSA-983189 | Kinesins |
| R-HSA-109582 | Hemostasis |
| R-HSA-1280218 | Adaptive Immune System |
| R-HSA-162582 | Signal Transduction |
| R-HSA-168256 | Immune System |
| R-HSA-194315 | Signaling by Rho GTPases |
| R-HSA-195258 | RHO GTPase Effectors |
| R-HSA-199991 | Membrane Trafficking |
| R-HSA-5653656 | Vesicle-mediated transport |
| R-HSA-6811442 | Intra-Golgi and retrograde Golgi-to-ER traffic |
| R-HSA-8856688 | Golgi-to-ER retrograde transport |
| R-HSA-9716542 | Signaling by Rho GTPases, Miro GTPases and RHOBTB3 |
| R-HSA-983231 | Factors involved in megakaryocyte development and platelet production |
MSigDB gene sets: 201 (showing top):
REACTOME_ADAPTIVE_IMMUNE_SYSTEM, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOCC_KINESIN_COMPLEX, TGACCTY_ERR1_Q2, REACTOME_MEMBRANE_TRAFFICKING, GGGTGGRR_PAX4_03, COUP_01, HNF4_DR1_Q3, CTGYNNCTYTAA_UNKNOWN, GOMF_CYTOSKELETAL_PROTEIN_BINDING, GOMF_KINESIN_BINDING, CHEN_METABOLIC_SYNDROM_NETWORK, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A
GO Biological Process (1): microtubule-based movement (GO:0007018)
GO Molecular Function (2): kinesin binding (GO:0019894), protein binding (GO:0005515)
GO Cellular Component (4): cytoplasm (GO:0005737), kinesin complex (GO:0005871), microtubule (GO:0005874), cytoskeleton (GO:0005856)
Reactome top-level categories
Rollup of top-12 pathways:
| Category | Pathways |
|---|---|
| Adaptive Immune System | 1 |
| RHO GTPase Effectors | 1 |
| Golgi-to-ER retrograde transport | 1 |
| Factors involved in megakaryocyte development and platelet production | 1 |
| Immune System | 1 |
| Signaling by Rho GTPases, Miro GTPases and RHOBTB3 | 1 |
| Signaling by Rho GTPases | 1 |
| Vesicle-mediated transport | 1 |
| Membrane Trafficking | 1 |
| Intra-Golgi and retrograde Golgi-to-ER traffic | 1 |
| Signal Transduction | 1 |
| Hemostasis | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| microtubule-based process | 1 |
| cytoskeletal protein binding | 1 |
| binding | 1 |
| intracellular anatomical structure | 1 |
| cellular anatomical structure | 1 |
| microtubule associated complex | 1 |
| microtubule cytoskeleton | 1 |
| polymeric cytoskeletal fiber | 1 |
| intracellular membraneless organelle | 1 |
Protein interactions and networks
STRING
2198 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| KLC4 | KIF5C | O60282 | 924 |
| KLC4 | MAPK8IP3 | Q9UPT6 | 924 |
| KLC4 | KIF5A | Q12840 | 916 |
| KLC4 | KIF5B | P33176 | 907 |
| KLC4 | MAPK8IP1 | Q9UQF2 | 906 |
| KLC4 | MAPK8IP2 | Q13387 | 886 |
| KLC4 | HAP1 | P54257 | 884 |
| KLC4 | CLSTN1 | O94985 | 880 |
| KLC4 | APP | P05067 | 801 |
| KLC4 | PLEKHM2 | Q8IWE5 | 769 |
| KLC4 | HTT | P42858 | 679 |
| KLC4 | TRAK2 | O60296 | 645 |
| KLC4 | ARL5B | Q96KC2 | 645 |
| KLC4 | DPYSL2 | Q16555 | 622 |
| KLC4 | KIF1A | Q12756 | 602 |
IntAct
197 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| YWHAZ | KLC4 | psi-mi:“MI:0915”(physical association) | 0.870 |
| YWHAQ | WDR62 | psi-mi:“MI:0914”(association) | 0.830 |
| YWHAH | ABLIM1 | psi-mi:“MI:0914”(association) | 0.800 |
| KRT31 | KLC4 | psi-mi:“MI:0915”(physical association) | 0.780 |
| KLC4 | KRT31 | psi-mi:“MI:0915”(physical association) | 0.780 |
| KRT31 | HGS | psi-mi:“MI:0914”(association) | 0.780 |
| KLC1 | KIF5B | psi-mi:“MI:0914”(association) | 0.730 |
| CDR2 | KTN1 | psi-mi:“MI:0914”(association) | 0.730 |
| KIF5B | KLC1 | psi-mi:“MI:0914”(association) | 0.730 |
| KLC4 | NECAB2 | psi-mi:“MI:0915”(physical association) | 0.720 |
| KLC4 | KATNAL1 | psi-mi:“MI:0915”(physical association) | 0.720 |
| NECAB2 | KLC4 | psi-mi:“MI:0915”(physical association) | 0.720 |
| KATNAL1 | KLC4 | psi-mi:“MI:0915”(physical association) | 0.720 |
| KLC4 | SYNE4 | psi-mi:“MI:0915”(physical association) | 0.670 |
| AZIN1 | OAZ2 | psi-mi:“MI:0914”(association) | 0.670 |
| KLC4 | YWHAE | psi-mi:“MI:0915”(physical association) | 0.650 |
| YWHAG | BLTP3B | psi-mi:“MI:2364”(proximity) | 0.640 |
| NUP43 | NUP98 | psi-mi:“MI:0914”(association) | 0.640 |
| YWHAH | PLEKHG3 | psi-mi:“MI:0914”(association) | 0.610 |
| YWHAB | BLTP3B | psi-mi:“MI:2364”(proximity) | 0.610 |
BioGRID (211): KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), KLC4 (Two-hybrid), SYNE4 (Two-hybrid), SLC16A9 (Two-hybrid), CEP57L1 (Two-hybrid), KLC4 (Affinity Capture-MS), KLC4 (Affinity Capture-MS)
ESM2 similar proteins: A0A8I6A2H6, A2AQ19, A4IG32, A5D7A0, D4A1F2, F1MF74, O12940, O14730, O35685, O43395, O43815, O55106, O60784, O88448, O88746, O94851, P08057, P13789, P19429, P50751, P70483, P97366, Q13435, Q17QG2, Q17QM6, Q1RMT7, Q2KIA6, Q3UJB0, Q4FZY0, Q5PQM2, Q5PYI0, Q5R5F1, Q5RDI4, Q63525, Q863B6, Q86XE3, Q8BML1, Q8MKD5, Q922U1, Q92541
Diamond homologs: O88447, O88448, P37285, P46822, P46824, P46825, Q05090, Q07866, Q2HJJ0, Q2TBQ9, Q5PQM2, Q5R581, Q5R8E2, Q68G30, Q6P597, Q91W40, Q9DBS5, Q9H0B6, Q9NSK0
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 125 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex | 8 | 65.5× | 5e-11 |
| Activation of BAD and translocation to mitochondria | 7 | 65.0× | 7e-10 |
| SARS-CoV-1 targets host intracellular signalling and regulatory pathways | 7 | 57.4× | 1e-09 |
| Activation of BH3-only proteins | 7 | 42.4× | 1e-08 |
| RHO GTPases activate PKNs | 7 | 27.1× | 2e-07 |
| Intrinsic Pathway for Apoptosis | 7 | 25.0× | 3e-07 |
| FOXO-mediated transcription | 5 | 20.5× | 7e-05 |
| SARS-CoV-1-host interactions | 8 | 17.1× | 5e-07 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| morphogenesis of an epithelium | 8 | 25.5× | 7e-07 |
| protein targeting | 7 | 23.7× | 7e-06 |
| microtubule-based movement | 6 | 16.4× | 3e-04 |
| intermediate filament organization | 7 | 15.6× | 9e-05 |
| negative regulation of TORC1 signaling | 5 | 15.0× | 2e-03 |
| epithelial cell differentiation | 6 | 9.8× | 4e-03 |
| intracellular protein localization | 9 | 8.7× | 2e-04 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
120 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 1 |
| Uncertain significance | 98 |
| Likely benign | 0 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (2)
| Variant ID | HGVS | Classification |
|---|---|---|
| 3772694 | NM_201521.3(KLC4):c.799_817del (p.Asn267fs) | Pathogenic |
| 1334583 | NM_201521.3(KLC4):c.553G>T (p.Glu185Ter) | Likely pathogenic |
SpliceAI
6634 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 6:43040913:A:AC | donor_gain | 1.0000 |
| 6:43040914:C:CC | donor_gain | 1.0000 |
| 6:43040914:CT:C | donor_gain | 1.0000 |
| 6:43040914:CTG:C | donor_gain | 1.0000 |
| 6:43040914:CTGGT:C | donor_gain | 1.0000 |
| 6:43041071:CTCAC:C | acceptor_gain | 1.0000 |
| 6:43041072:TCAC:T | acceptor_gain | 1.0000 |
| 6:43041073:CAC:C | acceptor_gain | 1.0000 |
| 6:43041073:CACC:C | acceptor_gain | 1.0000 |
| 6:43041074:AC:A | acceptor_gain | 1.0000 |
| 6:43041074:ACC:A | acceptor_loss | 1.0000 |
| 6:43041075:CC:C | acceptor_gain | 1.0000 |
| 6:43041083:A:AC | acceptor_gain | 1.0000 |
| 6:43042800:A:AC | donor_gain | 1.0000 |
| 6:43042801:C:CC | donor_gain | 1.0000 |
| 6:43042983:ACCT:A | acceptor_loss | 1.0000 |
| 6:43042984:CCTG:C | acceptor_loss | 1.0000 |
| 6:43042985:C:A | acceptor_loss | 1.0000 |
| 6:43042986:T:C | acceptor_loss | 1.0000 |
| 6:43043069:CCCA:C | donor_loss | 1.0000 |
| 6:43043070:CCAC:C | donor_loss | 1.0000 |
| 6:43043071:CA:C | donor_loss | 1.0000 |
| 6:43043072:ACC:A | donor_loss | 1.0000 |
| 6:43043073:CCTGC:C | donor_loss | 1.0000 |
| 6:43043177:CCTT:C | acceptor_loss | 1.0000 |
| 6:43043178:CTT:C | acceptor_gain | 1.0000 |
| 6:43043179:TT:T | acceptor_gain | 1.0000 |
| 6:43043179:TTCT:T | acceptor_loss | 1.0000 |
| 6:43043180:TC:T | acceptor_loss | 1.0000 |
| 6:43043181:C:CC | acceptor_gain | 1.0000 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000433413 (6:43072965 G>A), RS1000539582 (6:43067405 G>A,C), RS1000810369 (6:43060798 G>A), RS1001398014 (6:43068300 C>T), RS1001765872 (6:43068512 G>A,T), RS1001903542 (6:43072698 G>T), RS1002371743 (6:43071467 G>A), RS1002704714 (6:43059099 T>A), RS1002790431 (6:43071686 G>A), RS1002817891 (6:43062507 G>A), RS1003024272 (6:43068809 T>C), RS1003149481 (6:43063576 G>A), RS1003236245 (6:43058211 T>C), RS1003724330 (6:43063221 C>T), RS1003846183 (6:43070165 T>C)
Disease associations
OMIM: gene MIM:620909 | disease phenotypes: MIM:621129
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy | Limited | Autosomal recessive |
Mondo (1): early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy (MONDO:0700288)
Orphanet (0):
HPO phenotypes
31 total (30 of 31 shown, HPO-id order):
| HPO | Term |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000407 | Sensorineural hearing impairment |
| HP:0000510 | Rod-cone dystrophy |
| HP:0000543 | Optic disc pallor |
| HP:0000618 | Blindness |
| HP:0000639 | Nystagmus |
| HP:0000666 | Horizontal nystagmus |
| HP:0000762 | Decreased nerve conduction velocity |
| HP:0001256 | Mild intellectual disability |
| HP:0001257 | Spasticity |
| HP:0001271 | Polyneuropathy |
| HP:0001288 | Gait disturbance |
| HP:0001999 | Abnormal facial shape |
| HP:0002066 | Gait ataxia |
| HP:0002151 | Increased circulating lactate concentration |
| HP:0002169 | Clonus |
| HP:0002395 | Lower limb hyperreflexia |
| HP:0002505 | Loss of ambulation |
| HP:0002967 | Cubitus valgus |
| HP:0002987 | Elbow flexion contracture |
| HP:0003484 | Upper limb muscle weakness |
| HP:0003487 | Babinski sign |
| HP:0006380 | Knee flexion contracture |
| HP:0006466 | Ankle flexion contracture |
| HP:0007340 | Lower limb muscle weakness |
| HP:0007663 | Reduced visual acuity |
| HP:0010864 | Severe intellectual disability |
| HP:0011463 | Childhood onset |
| HP:0030211 | Slow pupillary light response |
| HP:0034392 | Joint contracture |
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST010083_171 | Hemoglobin levels | 1.000000e-09 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004509 | hemoglobin measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
40 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation, decreases expression, decreases methylation, increases methylation | 4 |
| bisphenol A | increases expression, affects expression, decreases expression | 3 |
| Acetaminophen | decreases expression | 2 |
| Quercetin | decreases expression, increases expression | 2 |
| Cyclosporine | decreases expression | 2 |
| Aflatoxin B1 | affects expression, decreases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| FR900359 | affects phosphorylation | 1 |
| 2,4,6-tribromophenol | decreases expression | 1 |
| methyleugenol | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| decabromobiphenyl ether | decreases expression | 1 |
| beta-lapachone | decreases expression, increases expression | 1 |
| tetrabromobisphenol A | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| perfluoro-n-nonanoic acid | decreases expression | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | decreases expression | 1 |
| 2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide | decreases expression, decreases reaction | 1 |
| hexabrominated diphenyl ether 153 | decreases expression | 1 |
| jinfukang | increases expression | 1 |
| Leflunomide | decreases expression | 1 |
| Arsenic | affects methylation | 1 |
| Vehicle Emissions | decreases expression, decreases reaction | 1 |
| Caffeine | affects phosphorylation | 1 |
| Cuprizone | affects cotreatment, increases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | decreases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Enzyme Inhibitors | decreases activity, increases O-linked glycosylation | 1 |
| Estradiol | decreases expression | 1 |
| Haloperidol | increases expression, affects cotreatment | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Associated diseases: early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): early-childhood-onset neurodegeneration with retinitis pigmentosa, sensorineural hearing loss, and demyelinating peripheral neuropathy