KHDRBS2

gene
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Also known as SLM1SLM-1MGC26664

Summary

KHDRBS2 (KH RNA binding domain containing, signal transduction associated 2, HGNC:18114) is a protein-coding gene on chromosome 6q11.1, encoding KH domain-containing, RNA-binding, signal transduction-associated protein 2 (Q5VWX1). RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion.

Predicted to enable mRNA binding activity and poly(A) binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be active in nucleus.

Source: NCBI Gene 202559 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 86 total
  • MANE Select transcript: NM_152688

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18114
Approved symbolKHDRBS2
NameKH RNA binding domain containing, signal transduction associated 2
Location6q11.1
Locus typegene with protein product
StatusApproved
AliasesSLM1, SLM-1, MGC26664
Ensembl geneENSG00000112232
Ensembl biotypeprotein_coding
OMIM610487
Entrez202559

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 nonsense_mediated_decay

ENST00000281156, ENST00000675091, ENST00000718012, ENST00000931671, ENST00000968831

RefSeq mRNA: 2 — MANE Select: NM_152688 NM_001350622, NM_152688

CCDS: CCDS4963

Canonical transcript exons

ENST00000281156 — 9 exons

ExonStartEnd
ENSE000007985136197806661978212
ENSE000007985146204787862047994
ENSE000009743116190124461901371
ENSE000009743126189463561894833
ENSE000011310506217718562177312
ENSE000012027166169719561697253
ENSE000012027276173268261732764
ENSE000012677396228585862286225
ENSE000040338896167996161681060

Expression profiles

Bgee: expression breadth ubiquitous, 102 present calls, max score 85.25.

FANTOM5 (CAGE): breadth broad, TPM avg 3.9392 / max 200.9506, expressed in 455 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
741973.6351454
741920.235955
741940.120754
741960.083152
741930.071938
741950.028415

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534385.25gold quality
corpus callosumUBERON:000233682.46gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.28gold quality
ganglionic eminenceUBERON:000402378.87gold quality
prefrontal cortexUBERON:000045177.75gold quality
superior frontal gyrusUBERON:000266177.33gold quality
nucleus accumbensUBERON:000188276.24gold quality
frontal cortexUBERON:000187074.89gold quality
primary visual cortexUBERON:000243674.30gold quality
cerebral cortexUBERON:000095672.70gold quality
dorsolateral prefrontal cortexUBERON:000983472.69gold quality
Brodmann (1909) area 9UBERON:001354072.50gold quality
vastus lateralisUBERON:000137972.40gold quality
cerebellar vermisUBERON:000472071.59gold quality
hypothalamusUBERON:000189871.58gold quality
anterior cingulate cortexUBERON:000983571.46gold quality
thyroid glandUBERON:000204670.30gold quality
left lobe of thyroid glandUBERON:000112069.97gold quality
caudate nucleusUBERON:000187369.97gold quality
putamenUBERON:000187469.63gold quality
right frontal lobeUBERON:000281069.07gold quality
ventricular zoneUBERON:000305368.63gold quality
right lobe of thyroid glandUBERON:000111968.41gold quality
epithelium of bronchusUBERON:000203167.67gold quality
brainUBERON:000095567.13gold quality
central nervous systemUBERON:000101766.88gold quality
lungUBERON:000204866.79gold quality
temporal lobeUBERON:000187166.63gold quality
Ammon’s hornUBERON:000195466.48gold quality
amygdalaUBERON:000187666.42gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-ANND-2yes3574.72
E-GEOD-180759yes1983.21
E-HCAD-35yes1923.50
E-HCAD-25yes91.64
E-ANND-3no3.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

113 targeting KHDRBS2, 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-4668-3P100.0068.742635
HSA-MIR-8485100.0077.574731
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692A100.0074.406850
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-318599.9968.121959
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-477599.9875.006394
HSA-MIR-806899.9873.852376
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-9-3P99.9670.882068
HSA-MIR-570-3P99.9672.414910
HSA-MIR-101-3P99.9475.032230
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-552-5P99.9368.561583
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-329-3P99.9166.561234
HSA-MIR-362-3P99.9166.381267

Literature-anchored findings (GeneRIF, showing 1)

  • molecular cloning and characterization (PMID:12549823)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_reriokhdrbs2ENSDARG00000069469
mus_musculusKhdrbs2ENSMUSG00000026058
rattus_norvegicusKhdrbs2ENSRNOG00000012284
drosophila_melanogasterqkr58E-3FBGN0022984
drosophila_melanogasterqkr58E-2FBGN0022985
drosophila_melanogasterqkr58E-1FBGN0022986
drosophila_melanogasterqkr54BFBGN0022987
drosophila_melanogasterCG4021FBGN0034659
drosophila_melanogasterCG10384FBGN0034731
drosophila_melanogasterCG3927FBGN0034739
drosophila_melanogasternsrFBGN0034740

Paralogs (4): QKI (ENSG00000112531), KHDRBS1 (ENSG00000121774), KHDRBS3 (ENSG00000131773), SF1 (ENSG00000168066)

Protein

Protein identifiers

KH domain-containing, RNA-binding, signal transduction-associated protein 2Q5VWX1 (reviewed: Q5VWX1)

Alternative names: Sam68-like mammalian protein 1

All UniProt accessions (2): Q5VWX1, A0A6Q8PGH5

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. Binds both poly(A) and poly(U) homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability. Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich exonic enhancer. Can regulate alternative splicing of NRXN1 in the laminin G-like domain 6 containing the evolutionary conserved neurexin alternative spliced segment 4 (AS4) involved in neurexin selective targeting to postsynaptic partners. Regulates cell-type specific alternative splicing of NRXN1 at AS4 and acts synergystically with SAM68 in exon skipping. In contrast acts antagonistically with SAM68 in NRXN3 exon skipping at AS4. Its phosphorylation by FYN inhibits its ability to regulate splice site selection. May function as an adapter protein for Src kinases during mitosis.

Subunit / interactions. Self-associates to form homooligomers. Interacts with KHDRBS1/SAM68; heterooligomer formation of KHDRBS family proteins may modulate RNA substrate specificity. Interacts with RBMX. Interacts with SAFB, SFRS9 and YTHDC1. Interacts with FYN and PLCG1 (via SH3 domain). Interacts (phosphorylated) with FYN, GRB2, PLCG1 and RASA1 (via SH2 domain).

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in brain, lung, kidney and small intestine. Weakly expressed in placenta, liver, spleen, thymus, ovary and colon.

Post-translational modifications. Methylated. Tyrosine phosphorylated by FYN, PTK6 and SRC. Tyrosine phosphorylated by SRC during mitosis.

Similarity. Belongs to the KHDRBS family.

RefSeq proteins (2): NP_001337551, NP_689901* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004087KH_domDomain
IPR032335Sam68-YYDomain
IPR032571Qua1_domDomain
IPR036612KH_dom_type_1_sfHomologous_superfamily
IPR045071BBP-likeFamily
IPR055256KH_1_KHDC4/BBP-likeDomain

Pfam: PF16274, PF16568, PF22675

UniProt features (11 total): sequence conflict 3, region of interest 2, modified residue 2, chain 1, domain 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5VWX1-F170.390.36

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 (2): 230, 240

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-8849468PTK6 Regulates Proteins Involved in RNA Processing
R-HSA-162582Signal Transduction
R-HSA-8848021Signaling by PTK6
R-HSA-9006927Signaling by Non-Receptor Tyrosine Kinases

MSigDB gene sets: 134 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, RORA1_01, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, AREB6_03, ATGTTAA_MIR302C, PUJANA_CHEK2_PCC_NETWORK, GOMF_SH2_DOMAIN_BINDING, AAAGACA_MIR511, GOBP_RNA_SPLICING, GOBP_REGULATION_OF_MRNA_SPLICING_VIA_SPLICEOSOME, GOBP_REGULATION_OF_RNA_SPLICING, TGGAAA_NFAT_Q4_01, ATGTAGC_MIR221_MIR222, GOMF_POLY_A_BINDING, GOMF_POLY_PYRIMIDINE_TRACT_BINDING

GO Biological Process (3): regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA processing (GO:0006397), regulation of mRNA splicing, via spliceosome (GO:0048024)

GO Molecular Function (8): mRNA binding (GO:0003729), poly(A) binding (GO:0008143), poly(U) RNA binding (GO:0008266), SH3 domain binding (GO:0017124), SH2 domain binding (GO:0042169), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Signaling by PTK61
Signaling by Non-Receptor Tyrosine Kinases1
Signal Transduction1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein domain specific binding2
binding2
alternative mRNA splicing, via spliceosome1
regulation of mRNA splicing, via spliceosome1
RNA processing1
mRNA metabolic process1
mRNA splicing, via spliceosome1
regulation of RNA splicing1
regulation of mRNA processing1
RNA binding1
poly-purine tract binding1
poly-pyrimidine tract binding1
nucleic acid binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

1256 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KHDRBS2CRYL1Q9Y2S2817
KHDRBS2PRMT1Q99873732
KHDRBS2PTK6Q13882591
KHDRBS2LGSNQ5TDP6557
KHDRBS2ESRP1Q6NXG1516
KHDRBS2ESRP2Q9H6T0504
KHDRBS2TFEBP19484492
KHDRBS2ARHGAP9Q9BRR9483
KHDRBS2KHSRPQ92945476
KHDRBS2RBMXP38159474
KHDRBS2MITFO75030473
KHDRBS2SERPINA4P29622467
KHDRBS2C4orf33Q8N1A6460
KHDRBS2ZNF540Q8NDQ6447
KHDRBS2HNRNPMP52272431
KHDRBS2HNRNPA0Q13151431

IntAct

216 interactions, top by confidence:

ABTypeScore
RBMXKHDRBS2psi-mi:“MI:0915”(physical association)0.850
KHDRBS2RBMXpsi-mi:“MI:0915”(physical association)0.850
KHDRBS2RBM3psi-mi:“MI:0915”(physical association)0.830
RBM3KHDRBS2psi-mi:“MI:0915”(physical association)0.830
KHDRBS3KHDRBS2psi-mi:“MI:0915”(physical association)0.800
PRPF31KHDRBS2psi-mi:“MI:0915”(physical association)0.790
KHDRBS2PRPF31psi-mi:“MI:0915”(physical association)0.790
KHDRBS2TYK2psi-mi:“MI:0915”(physical association)0.780
TYK2KHDRBS2psi-mi:“MI:0915”(physical association)0.780
KHDRBS2SDCBPpsi-mi:“MI:0915”(physical association)0.720
KHDRBS2PRR3psi-mi:“MI:0915”(physical association)0.720
KHDRBS2CATSPER1psi-mi:“MI:0915”(physical association)0.720
DOCK2KHDRBS2psi-mi:“MI:0915”(physical association)0.720
YTHDC1KHDRBS2psi-mi:“MI:0915”(physical association)0.720

BioGRID (203): KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid), KHDRBS2 (Two-hybrid)

ESM2 similar proteins: B2GV05, B5FXN8, G3V9R8, O08583, O75525, O77768, P07910, P19600, P23588, P52756, P55795, P70333, P97379, P97855, Q08DJ0, Q0VFL7, Q13148, Q13283, Q1RMU5, Q28FB9, Q32LC7, Q3SZF3, Q3T0I4, Q58EA2, Q5R5W2, Q5R9L3, Q5RA82, Q5RB87, Q5RD26, Q5SRX1, Q5VWX1, Q5ZLN5, Q60HC3, Q64012, Q6AY09, Q6GLW1, Q86SE5, Q86V81, Q8BGD9, Q8BTF8

Diamond homologs: G5EFF1, O01367, O74555, O75525, P0CO44, P0CO45, P13230, Q07666, Q08BJ2, Q0VFL3, Q0WLR1, Q12186, Q15637, Q17339, Q32NN2, Q4P0H7, Q4WXV6, Q54BM5, Q5AED9, Q5VWX1, Q5W9D5, Q5W9D6, Q5W9D7, Q60749, Q64213, Q6BSP4, Q6C187, Q6FW77, Q6IRN2, Q6P0D0, Q6P104, Q750X2, Q75GR5, Q7JJZ8, Q8GWR3, Q8GYR4, Q8NIW7, Q8UUW7, Q91V33, Q91XU1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 59 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:

PathwayPartnersFoldFDR
mRNA Splicing - Major Pathway69.1×5e-03

GO biological processes:

GO termPartnersFoldFDR
positive regulation of mRNA splicing, via spliceosome555.5×5e-06
regulation of alternative mRNA splicing, via spliceosome734.9×4e-07
mRNA splicing, via spliceosome814.9×6e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance68
Likely benign4
Benign6

Top pathogenic / likely-pathogenic (0)

SpliceAI

5929 predictions. Top by Δscore:

VariantEffectΔscore
6:61697251:ACA:Aacceptor_gain1.0000
6:61697252:CA:Cacceptor_gain1.0000
6:61697252:CAC:Cacceptor_gain1.0000
6:61697254:C:CCacceptor_gain1.0000
6:61707328:A:ACdonor_gain1.0000
6:61707329:C:CCdonor_gain1.0000
6:61732676:CCTTA:Cdonor_loss1.0000
6:61732677:CTTA:Cdonor_loss1.0000
6:61732678:TTA:Tdonor_loss1.0000
6:61732679:TACCT:Tdonor_loss1.0000
6:61732680:A:ACdonor_gain1.0000
6:61732680:A:AGdonor_loss1.0000
6:61732680:AC:Adonor_gain1.0000
6:61732681:C:Adonor_loss1.0000
6:61732681:C:CCdonor_gain1.0000
6:61732681:CC:Cdonor_gain1.0000
6:61732681:CCT:Cdonor_gain1.0000
6:61732760:TAACC:Tacceptor_gain1.0000
6:61732761:AACC:Aacceptor_gain1.0000
6:61732762:ACC:Aacceptor_gain1.0000
6:61732763:CC:Cacceptor_gain1.0000
6:61732763:CCC:Cacceptor_gain1.0000
6:61732763:CCCTG:Cacceptor_loss1.0000
6:61732764:CC:Cacceptor_gain1.0000
6:61732765:C:CAacceptor_loss1.0000
6:61732765:C:CCacceptor_gain1.0000
6:61732765:C:Tacceptor_gain1.0000
6:61732766:T:Aacceptor_loss1.0000
6:61732771:C:CTacceptor_gain1.0000
6:61732772:A:Tacceptor_gain1.0000

AlphaMissense

2245 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:61901331:A:GL175S1.000
6:61901335:C:TE174K1.000
6:61901340:A:GL172P1.000
6:61901342:T:AQ171H1.000
6:61901342:T:GQ171H1.000
6:61901343:T:GQ171P1.000
6:61901355:A:CI167S1.000
6:61901355:A:GI167T1.000
6:61901360:A:CD165E1.000
6:61901360:A:TD165E1.000
6:61901361:T:AD165V1.000
6:61901361:T:CD165G1.000
6:61901361:T:GD165A1.000
6:61901362:C:AD165Y1.000
6:61901362:C:GD165H1.000
6:61978067:G:TP161H1.000
6:61978073:A:GL159P1.000
6:61978073:A:TL159Q1.000
6:61978075:G:CF158L1.000
6:61978075:G:TF158L1.000
6:61978076:A:GF158S1.000
6:61978077:A:GF158L1.000
6:61978097:G:TA151E1.000
6:61978109:C:GR147P1.000
6:61978118:G:TA144D1.000
6:61978145:A:TI135N1.000
6:61978151:A:TV133E1.000
6:61978154:T:GH132P1.000
6:61978157:A:GL131P1.000
6:61978157:A:TL131H1.000

dbSNP variants (sampled 300 via entrez): RS1000000425 (6:61660266 G>A,C), RS1000001003 (6:62188974 G>A,T), RS1000002348 (6:61937701 C>A,T), RS1000009440 (6:61681119 A>G,T), RS1000015220 (6:62076848 C>A), RS1000022092 (6:61590615 C>T), RS1000040824 (6:61576588 T>A,C), RS1000044133 (6:61734413 C>T), RS1000046548 (6:62077063 A>G), RS1000049020 (6:61899058 T>C), RS1000050461 (6:62028267 T>A,C), RS1000051669 (6:61590448 T>G), RS1000059590 (6:61893354 A>G), RS1000064486 (6:61739730 A>C), RS1000068538 (6:62241448 A>C)

Disease associations

OMIM: gene MIM:610487 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

StudyTraitp-value
GCST000189_38Protein quantitative trait loci3.000000e-07
GCST003563_7Presence of antiphospholipid antibodies4.000000e-06
GCST003739_2Esophageal adenocarcinoma2.000000e-08
GCST003740_8Barrett’s esophagus or Esophageal adenocarcinoma3.000000e-09
GCST004735_23Epstein-Barr virus copy number in lymphoblastoid cell lines2.000000e-06
GCST004735_24Epstein-Barr virus copy number in lymphoblastoid cell lines9.000000e-06
GCST004735_25Epstein-Barr virus copy number in lymphoblastoid cell lines4.000000e-07
GCST007157_4Corneal astigmatism4.000000e-06
GCST007576_279Chronotype3.000000e-13

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004736aspartate aminotransferase measurement
EFO:1002040Corneal astigmatism
EFO:0008328chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, decreases methylation2
bisphenol Aincreases methylation1
terbufosincreases methylation1
aflatoxin B2increases methylation1
Resveratrolaffects cotreatment, decreases expression1
Acetaminophenincreases expression1
Vehicle Emissionsdecreases methylation1
Benzo(a)pyreneincreases methylation1
Copperaffects cotreatment, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Fonofosincreases methylation1
Estradiolaffects binding, increases reaction1
Parathionincreases methylation1
Rotenoneincreases expression1
Aflatoxin B1decreases methylation1
Genisteinaffects binding, increases reaction1

Clinical trials (associated diseases)

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