KCNU1

gene
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Also known as KCa5.1Slo3KCNMC1Kcnma3

Summary

KCNU1 (potassium calcium-activated channel subfamily U member 1, HGNC:18867) is a protein-coding gene on chromosome 8p11.23, encoding Potassium channel subfamily U member 1 (A8MYU2). Testis-specific potassium channel activated by both intracellular pH and membrane voltage that mediates export of K(+).

This gene encodes a member of the potassium channel family of proteins. The encoded voltage-gated ion channel allows the outward flow of potassium ions during plasma membrane hyperpolarization in sperm. Opening of this channel may be regulated by calcium ion levels. Homozygous knockout mice that lack the related mouse gene exhibit male sterility. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 157855 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): spermatogenic failure 79 (Limited, GenCC)
  • GWAS associations: 16
  • Clinical variants (ClinVar): 183 total — 3 pathogenic
  • Phenotypes (HPO): 6
  • Druggable target: yes
  • MANE Select transcript: NM_001031836

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18867
Approved symbolKCNU1
Namepotassium calcium-activated channel subfamily U member 1
Location8p11.23
Locus typegene with protein product
StatusApproved
AliasesKCa5.1, Slo3, KCNMC1, Kcnma3
Ensembl geneENSG00000215262
Ensembl biotypeprotein_coding
OMIM615215
Entrez157855

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000399881, ENST00000518904, ENST00000522372, ENST00000522417, ENST00000523973

RefSeq mRNA: 1 — MANE Select: NM_001031836 NM_001031836

CCDS: CCDS55220

Canonical transcript exons

ENST00000399881 — 27 exons

ExonStartEnd
ENSE000015405783692249036922629
ENSE000015405793691882336918897
ENSE000015405853691093036911119
ENSE000015405863690931136909535
ENSE000015405873690570836905804
ENSE000015405993684580236845899
ENSE000015406023684558036845669
ENSE000015406063684093236841003
ENSE000015406083684046336840575
ENSE000015406103683679336836945
ENSE000015406133683629636836365
ENSE000015406153683478636834868
ENSE000015406183683355436833659
ENSE000015406213681765036817760
ENSE000015406253681559636815687
ENSE000015406283681420736814377
ENSE000015406303680871836808793
ENSE000015406333680737536807450
ENSE000015406463680402736804088
ENSE000016139593678730636787425
ENSE000017028423686440436864521
ENSE000020895973693551536936125
ENSE000020906783678437436784605
ENSE000034641333693292036933032
ENSE000034651013693095136931145
ENSE000034795913680519536805285
ENSE000035986573680626936806380

Expression profiles

Bgee: expression breadth broad, 60 present calls, max score 87.55.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0126 / max 10.0930, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
884110.00653
884120.00613

Top tissues by expression

222 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001987.55gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.54gold quality
left testisUBERON:000453367.52gold quality
right testisUBERON:000453467.13gold quality
testisUBERON:000047367.00gold quality
pancreatic ductal cellCL:000207964.11silver quality
epithelial cell of pancreasCL:000008355.15gold quality
cardiac muscle of right atriumUBERON:000337954.34gold quality
left ventricle myocardiumUBERON:000656654.23gold quality
kidney epitheliumUBERON:000481953.93gold quality
upper arm skinUBERON:000426353.52gold quality
tibialis anteriorUBERON:000138551.72silver quality
deltoidUBERON:000147651.48gold quality
myocardiumUBERON:000234950.25gold quality
bone marrow cellCL:000209249.62gold quality
lower esophagus mucosaUBERON:003583449.31gold quality
adult organismUBERON:000702348.43silver quality
ileal mucosaUBERON:000033147.76silver quality
nasal cavity epitheliumUBERON:000538447.03gold quality
quadriceps femorisUBERON:000137746.95gold quality
caput epididymisUBERON:000435845.88gold quality
vastus lateralisUBERON:000137945.40gold quality
skin of hipUBERON:000155444.89silver quality
layer of synovial tissueUBERON:000761643.55gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
secondary oocyteCL:000065542.57gold quality
muscle tissueUBERON:000238542.30gold quality
lower lobe of lungUBERON:000894942.13silver quality
skeletal muscle tissueUBERON:000113441.46gold quality
superficial temporal arteryUBERON:000161441.33gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting KCNU1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-684499.8270.692423
HSA-MIR-182599.7268.111089
HSA-MIR-199A-5P99.5169.711107
HSA-MIR-199B-5P99.5169.741098
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-377-3P99.3770.181905
HSA-MIR-608899.2968.451284
HSA-MIR-10522-5P99.2668.502087
HSA-MIR-2115-5P98.6668.071191
HSA-MIR-6784-3P98.3964.88662
HSA-MIR-4768-3P98.1666.022330
HSA-MIR-6862-3P97.9264.86531
HSA-MIR-3664-3P97.8567.621452

Literature-anchored findings (GeneRIF, showing 6)

  • These results present insights into the function of a protein expected to be critical for human reproduction and provide a framework to study the mechanism of pH gating in SLO3 channels. (PMID:23129643)
  • The authors conclude that Slo3 represents the principal K(+) channel in human sperm that carries the Ca(2+)-activated IKSper current. (PMID:24670955)
  • results suggest that sperm-specific genes can evolve rapidly and that natural genetic variation may have led to a SLO3 variant that differs from wild type in both pH and intracellular Ca(2+) sensitivities. (PMID:28377504)
  • Homozygous mutation in SLO3 leads to severe asthenoteratozoospermia due to acrosome hypoplasia and mitochondrial sheath malformations. (PMID:34980136)
  • Bi-allelic variants in KCNU1 cause impaired acrosome reactions and male infertility. (PMID:35551387)
  • Transmembrane determinants of voltage-gating differences between BK (Slo1) and Slo3 channels. (PMID:38637987)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusKcnu1ENSMUSG00000031576
rattus_norvegicusKcnu1ENSRNOG00000014741
drosophila_melanogasterSLO2FBGN0261698
caenorhabditis_elegansWBGENE00004831

Paralogs (3): KCNT1 (ENSG00000107147), KCNMA1 (ENSG00000156113), KCNT2 (ENSG00000162687)

Protein

Protein identifiers

Potassium channel subfamily U member 1A8MYU2 (reviewed: A8MYU2)

Alternative names: Calcium-activated potassium channel subunit alpha-3, Calcium-activated potassium channel, subfamily M subunit alpha-3, KCa5, Slowpoke homolog 3

All UniProt accessions (4): A8MYU2, E5RGP7, E5RHP1, E5RJA6

UniProt curated annotations — full annotation on UniProt →

Function. Testis-specific potassium channel activated by both intracellular pH and membrane voltage that mediates export of K(+). Represents the primary spermatozoan K(+) current. The channel underlies a pH-triggered membrane hyperpolarization during the process of sperm capacitation, as sperm encounter the alkaline environment near the ovum in the female reproductive tract, thereby playing an essential for male fertility.

Subunit / interactions. Homotetramer; which constitutes the activated potassium channel. Interacts with LRRC52; this interaction changes channel gating properties, such as shifting gating to more negative potentials at a given pH.

Subcellular location. Cell membrane. Cell projection. Cilium. Flagellum membrane.

Tissue specificity. Testis-specific.

Disease relevance. Spermatogenic failure 79 (SPGF79) [MIM:620196] An autosomal recessive, male infertility disorder characterized by asthenoteratozoospermia with acrosome hypoplasia, disruption of the mitochondrial sheath, and reduced progressive sperm motility. The disorder is due to an abnormal acrosome reaction and impaired membrane potential after capacitation. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Regulated by changes in cytosolic pH; activated by alkalization. Activated by intracellular Ca(2+). Despite strong sequence similarity, human KCNU1 channels are significantly more sensitive to activation by internal Ca(2+) and less pH-sensitive than mouse KCNU1. VU0546110 acts as a selective inhibitor. The auxiliary subunit LRRC52 shifts the activation of KCNU1 to more negative potentials at a given pH.

Domain organisation. The S4 segment, which is characterized by a series of positively charged amino acids at every third position, is part of the voltage-sensor. The pore-forming domain (also referred as P region) is imbedded into the membrane, and forms the selectivity filter of the pore. It contains the signature sequence of potassium channels that displays selectivity to potassium. The RCK N-terminal domain mediates the homotetramerization, thereby promoting the assembly of monomers into functional potassium channel. The C-terminal cytosolic region confers the pH-dependence.

Similarity. Belongs to the potassium channel family. Calcium-activated (TC 1.A.1.3) subfamily. KCa5.1/KCNU1 sub-subfamily.

RefSeq proteins (1): NP_001027006* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003148RCK_NDomain
IPR003929K_chnl_BK_asuDomain
IPR005821Ion_trans_domDomain
IPR047871K_chnl_Slo-likeFamily
IPR048735Slowpoke-like_CDomain

Pfam: PF00520, PF03493, PF21014, PF22614

Catalyzed reactions (Rhea), 1 shown:

  • K(+)(in) = K(+)(out) (RHEA:29463)

UniProt features (87 total): helix 31, strand 22, topological domain 9, transmembrane region 7, sequence variant 5, turn 3, domain 2, region of interest 2, compositionally biased region 2, chain 1, intramembrane region 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4HPFX-RAY DIFFRACTION3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A8MYU2-F174.460.33

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-1300642Sperm Motility And Taxes
R-HSA-1187000Fertilization
R-HSA-1474165Reproduction

MSigDB gene sets: 74 (showing top): GOBP_POTASSIUM_ION_TRANSPORT, TSENG_IRS1_TARGETS_UP, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_MONOATOMIC_CATION_TRANSPORT, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_MOTILE_CILIUM, GOCC_TRANSPORTER_COMPLEX, GOCC_MEMBRANE_PROTEIN_COMPLEX, GOCC_CILIUM, GOMF_CALCIUM_ACTIVATED_POTASSIUM_CHANNEL_ACTIVITY, GOMF_METAL_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY

GO Biological Process (6): reproductive process (GO:0022414), potassium ion transmembrane transport (GO:0071805), monoatomic ion transport (GO:0006811), potassium ion transport (GO:0006813), monoatomic ion transmembrane transport (GO:0034220), transmembrane transport (GO:0055085)

GO Molecular Function (2): potassium channel activity (GO:0005267), monoatomic ion channel activity (GO:0005216)

GO Cellular Component (7): plasma membrane (GO:0005886), membrane (GO:0016020), monoatomic ion channel complex (GO:0034702), sperm flagellum (GO:0036126), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Fertilization1
Reproduction1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport2
cellular anatomical structure2
biological_process1
potassium ion transport1
monoatomic cation transmembrane transport1
metal ion transport1
monoatomic ion transport1
transmembrane transport1
cellular process1
monoatomic cation channel activity1
potassium ion transmembrane transporter activity1
monoatomic ion transmembrane transporter activity1
channel activity1
membrane1
cell periphery1
transmembrane transporter complex1
9+2 motile cilium1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
cilium1

Protein interactions and networks

STRING

960 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KCNU1LRRC52Q8N7C0915
KCNU1CATSPER1Q8NEC5717
KCNU1SLC9C1Q4G0N8687
KCNU1KCNMB4Q86W47636
KCNU1LRRC26Q2I0M4630
KCNU1HVCN1Q96D96622
KCNU1KCNN1Q92952603
KCNU1LRRC38Q5VT99584
KCNU1KCNN4O15554560
KCNU1LRRC55Q6ZSA7535
KCNU1KCNMB1P78475526
KCNU1KCNN2Q9H2S1507
KCNU1CSN3P07498506
KCNU1CATSPER4Q7RTX7487
KCNU1EFCAB9A8MZ26460

IntAct

1 interactions, top by confidence:

ABTypeScore
KCNU1KCNU1psi-mi:“MI:0407”(direct interaction)0.440

ESM2 similar proteins: A0A1D8PTL7, A2WNZ9, A2YGP9, A5LFX5, A8MYU2, D4A6Z8, F4HWB6, O14197, O16242, O54982, O60146, O95069, P28584, P38329, P40310, P47144, P47564, P47946, P75323, P87122, P92960, P97438, Q0D9S3, Q0JNB6, Q10065, Q10937, Q38849, Q38898, Q54DA4, Q653P0, Q6H501, Q6SZ87, Q759P7, Q7XPF7, Q7XPF8, Q7XUW4, Q84TI7, Q8L481, Q8L4K5, Q920B6

Diamond homologs: A5LFX5, A8MYU2, B7ZC96, D4A6Z8, O18866, O18867, O54982, Q03720, Q08460, Q12791, Q28204, Q28265, Q57603, Q62976, Q8AYS8, Q90ZC7, Q95V25, Q9BG98, A0A509AS68, D3Z649, O17185, O35174, O43526, O88943, P31069, P56696, Q57604, Q5JUK3, Q69TN4, Q6UVM3, Q6UVM4, Q6ZPR4, Q8I5E6, Q8IKI3, Q8LIN5, Q8QFV0, Q92953, Q979Z2, Q9ER26, Q9FWX6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

183 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic3
Likely pathogenic0
Uncertain significance154
Likely benign14
Benign6

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
2443714NM_001031836.3(KCNU1):c.1237A>T (p.Ile413Phe)Pathogenic
2443715NM_001031836.3(KCNU1):c.2144A>G (p.His715Arg)Pathogenic
2443716NM_001031836.3(KCNU1):c.1295+3A>CPathogenic

SpliceAI

4947 predictions. Top by Δscore:

VariantEffectΔscore
8:36784589:G:Tdonor_gain1.0000
8:36784595:G:GTdonor_gain1.0000
8:36787426:G:GGdonor_gain1.0000
8:36805193:A:AGacceptor_gain1.0000
8:36805194:G:GAacceptor_gain1.0000
8:36805194:GC:Gacceptor_gain1.0000
8:36805194:GCC:Gacceptor_gain1.0000
8:36805194:GCCCT:Gacceptor_gain1.0000
8:36806260:A:AGacceptor_gain1.0000
8:36806261:T:Gacceptor_gain1.0000
8:36806265:A:AGacceptor_gain1.0000
8:36806266:T:Gacceptor_gain1.0000
8:36806267:A:AGacceptor_gain1.0000
8:36806268:G:GTacceptor_gain1.0000
8:36806268:GT:Gacceptor_gain1.0000
8:36806268:GTT:Gacceptor_gain1.0000
8:36806268:GTTT:Gacceptor_gain1.0000
8:36806268:GTTTA:Gacceptor_gain1.0000
8:36806376:GCTAG:Gdonor_gain1.0000
8:36806377:CTAGG:Cdonor_loss1.0000
8:36806378:TAGG:Tdonor_loss1.0000
8:36806381:G:GGdonor_gain1.0000
8:36806381:GTAA:Gdonor_loss1.0000
8:36806382:TAAG:Tdonor_loss1.0000
8:36808716:A:AGacceptor_gain1.0000
8:36808717:G:GAacceptor_gain1.0000
8:36814370:G:GTdonor_gain1.0000
8:36814370:G:Tdonor_gain1.0000
8:36815590:TTTTA:Tacceptor_loss1.0000
8:36815591:TTTAG:Tacceptor_loss1.0000

AlphaMissense

7540 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:36932993:G:CR1002P0.997
8:36814372:A:CS300R0.996
8:36814374:T:AS300R0.996
8:36814374:T:GS300R0.996
8:36807383:T:CF197L0.995
8:36807385:C:AF197L0.995
8:36807385:C:GF197L0.995
8:36808758:A:CS233R0.995
8:36808760:T:AS233R0.995
8:36808760:T:GS233R0.995
8:36808792:T:CL244P0.994
8:36814343:G:CR290P0.994
8:36817751:T:CF366S0.994
8:36804048:A:CS113R0.993
8:36804050:C:AS113R0.993
8:36804050:C:GS113R0.993
8:36806296:T:CF166L0.993
8:36806298:C:AF166L0.993
8:36806298:C:GF166L0.993
8:36817748:T:AV365D0.993
8:36840560:T:CF539S0.993
8:36805265:A:CS150R0.992
8:36805267:T:AS150R0.992
8:36805267:T:GS150R0.992
8:36814339:G:AG289R0.992
8:36814339:G:CG289R0.992
8:36840559:T:CF539L0.992
8:36840561:T:AF539L0.992
8:36840561:T:GF539L0.992
8:36817661:T:AV336D0.991

dbSNP variants (sampled 300 via entrez): RS1000012784 (8:36913095 A>G), RS1000022124 (8:36898721 G>A), RS1000028298 (8:36847310 C>T), RS1000079206 (8:36852769 T>C,G), RS1000084816 (8:36787813 CTAATTATA>C), RS1000105690 (8:36888391 C>T), RS1000112739 (8:36897696 C>T), RS1000118004 (8:36894678 C>A,T), RS1000143268 (8:36807018 G>A), RS1000144212 (8:36796347 G>A,T), RS1000148162 (8:36812183 C>T), RS1000170693 (8:36894458 C>A,G,T), RS1000175652 (8:36796086 G>A), RS1000215773 (8:36904460 C>T), RS1000228625 (8:36904389 T>C)

Disease associations

OMIM: gene MIM:615215 | disease phenotypes: MIM:620196

GenCC curated gene-disease

DiseaseClassificationInheritance
spermatogenic failure 79LimitedAutosomal recessive

Mondo (1): spermatogenic failure 79 (MONDO:0859352)

Orphanet (0):

HPO phenotypes

6 total (6 of 6 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000798Oligozoospermia
HP:0003251Male infertility
HP:0011462Young adult onset
HP:0012207Reduced sperm motility
HP:0032560Coiled sperm flagella

GWAS associations

16 associations (top):

StudyTraitp-value
GCST001208_12Insulin resistance/response2.000000e-06
GCST001585_3Breast size2.000000e-14
GCST002932_3Manganese levels5.000000e-06
GCST002932_37Manganese levels4.000000e-06
GCST003124_28Mild influenza (H1N1) infection1.000000e-09
GCST003985_8Breast size7.000000e-31
GCST004894_142Type 2 diabetes3.000000e-09
GCST006445_3Femoral neck bone mineral density8.000000e-07
GCST006655_10Breast size6.000000e-09
GCST006655_9Breast size1.000000e-08
GCST006666_3Lipid traits (pleiotropy) (HIPO component 1)4.000000e-09
GCST006867_69Type 2 diabetes4.000000e-11
GCST007159_27Corneal astigmatism5.000000e-06
GCST010118_160Type 2 diabetes2.000000e-10
GCST011342_10Body fat percentage and triglycerides (pairwise)3.000000e-08
GCST90000047_152Age at first sexual intercourse2.000000e-08

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:1001488influenza A (H1N1)
EFO:0007785femoral neck bone mineral density
EFO:0004530triglyceride measurement
EFO:0004574total cholesterol measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:1002040Corneal astigmatism
EFO:0007800body fat percentage
EFO:0009749age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4524132 (PROTEIN FAMILY)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: vgic — Calcium- and sodium-activated potassium channels (KCa, KNa)

Most potent curated ligand interactions (1 total), top 1:

LigandActionAffinityParameter
VU0546110Channel blocker5.89pIC50

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression1
N-acetyl-4-benzoquinoneimineaffects response to substance1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, affects response to substance, increases expression1
abrinedecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Arsenic Trioxideincreases expression1
Rosmarinic Aciddecreases activity1
Benzo(a)pyreneaffects methylation, increases methylation1
Copperaffects cotreatment, decreases expression1
Lipopolysaccharidesaffects response to substance, increases expression, affects cotreatment1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4880152BindingSK+ channel CEREP ligand profilingData for DCP probe A-079

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.