SLF1

gene
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Also known as DKFZp761C121DKFZp564C0469BRCTxhNSE5

Summary

SLF1 (SMC5/6 complex localization factor 1, HGNC:25408) is a protein-coding gene on chromosome 5q15, encoding SMC5-SMC6 complex localization factor protein 1 (Q9BQI6). Plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance.

Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in nucleoplasm and site of double-strand break.

Source: NCBI Gene 84250 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 171 total
  • MANE Select transcript: NM_032290

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25408
Approved symbolSLF1
NameSMC5/6 complex localization factor 1
Location5q15
Locus typegene with protein product
StatusApproved
AliasesDKFZp761C121, DKFZp564C0469, BRCTx, hNSE5
Ensembl geneENSG00000133302
Ensembl biotypeprotein_coding
OMIM618467
Entrez84250

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 9 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000265140, ENST00000450932, ENST00000466957, ENST00000475916, ENST00000493934, ENST00000504099, ENST00000508130, ENST00000508383, ENST00000908676, ENST00000939302, ENST00000939303, ENST00000939304, ENST00000939305, ENST00000966409, ENST00000966410

RefSeq mRNA: 1 — MANE Select: NM_032290 NM_032290

CCDS: CCDS4071

Canonical transcript exons

ENST00000265140 — 21 exons

ExonStartEnd
ENSE000018370849469483194697621
ENSE000018440629461866994618765
ENSE000022032419465463094654752
ENSE000022051799467084394671008
ENSE000022272559463050394630743
ENSE000022337729467015194670279
ENSE000022519609466586194666024
ENSE000022737719467880894678955
ENSE000022860079464327394643435
ENSE000034599249462881194628924
ENSE000034614099466229894662351
ENSE000034899709465170294651845
ENSE000034942059468947394689606
ENSE000035416369468657394686718
ENSE000035609469468850694688669
ENSE000035729719465327294653421
ENSE000035760489466375094663908
ENSE000035856229464945494649597
ENSE000036135529462909294629167
ENSE000036461809469207494692256
ENSE000036760979469156494691656

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 95.05.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.8117 / max 488.0229, expressed in 1599 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
5760511.03191588
576081.1382145
576060.5166275
576100.105134
576090.01997

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065595.05gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047394.90gold quality
oocyteCL:000002392.18gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.14gold quality
middle temporal gyrusUBERON:000277187.41gold quality
ventricular zoneUBERON:000305387.23gold quality
Brodmann (1909) area 46UBERON:000648386.92gold quality
cerebellar hemisphereUBERON:000224585.39gold quality
cerebellar cortexUBERON:000212985.32gold quality
calcaneal tendonUBERON:000370185.20gold quality
cerebellumUBERON:000203785.10gold quality
right hemisphere of cerebellumUBERON:001489084.82gold quality
ganglionic eminenceUBERON:000402384.81gold quality
embryoUBERON:000092284.80gold quality
cortical plateUBERON:000534384.11gold quality
testisUBERON:000047382.57gold quality
cerebellar vermisUBERON:000472082.45gold quality
right testisUBERON:000453481.82gold quality
bone marrowUBERON:000237181.81gold quality
Brodmann (1909) area 9UBERON:001354081.53gold quality
bronchial epithelial cellCL:000232881.46gold quality
dorsolateral prefrontal cortexUBERON:000983481.32gold quality
left testisUBERON:000453381.13gold quality
bone marrow cellCL:000209280.98gold quality
right frontal lobeUBERON:000281080.92gold quality
sural nerveUBERON:001548880.86gold quality
granulocyteCL:000009480.29gold quality
bronchusUBERON:000218580.23gold quality
superior frontal gyrusUBERON:000266179.91gold quality
frontal cortexUBERON:000187079.76gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-8894yes461.87
E-ANND-3yes4.88
E-GEOD-109979no203.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting SLF1, 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-8485100.0077.574731
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-477599.9875.006394
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-590-3P99.9674.346478
HSA-MIR-338-5P99.9272.342951
HSA-MIR-205-3P99.9269.923165
HSA-MIR-568099.9169.833421
HSA-MIR-589-3P99.9169.622088
HSA-MIR-95-5P99.8972.173973
HSA-MIR-153-5P99.8973.866317
HSA-MIR-3140-3P99.8868.472069
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-570099.6469.882280
HSA-MIR-4666A-5P99.4169.721887
HSA-MIR-426399.1869.252236
HSA-MIR-125399.1267.081688
HSA-MIR-670-3P99.0368.882404
HSA-MIR-455-3P98.9467.68878
HSA-MIR-4724-5P98.8767.751324
HSA-MIR-314998.7767.131639
HSA-MIR-6773-3P98.1765.511213
HSA-MIR-4659B-5P98.0366.84979
HSA-MIR-4659A-5P98.0366.42819
HSA-MIR-3620-3P97.7864.88772
HSA-MIR-4700-3P97.7468.641014
HSA-MIR-430897.5667.131385
HSA-MIR-937-5P97.4368.39667
HSA-MIR-215-3P97.0268.011209
HSA-MIR-367497.0168.861171

Literature-anchored findings (GeneRIF, showing 1)

  • Results describe the cloning, characterization, and targeted mutagenesis of Brctx, a novel gene with a BRCT motif [Brctx]. (PMID:15632077)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioslf1ENSDARG00000102118
mus_musculusSlf1ENSMUSG00000021597
rattus_norvegicusSlf1ENSRNOG00000040279

Paralogs (1): TOPBP1 (ENSG00000163781)

Protein

Protein identifiers

SMC5-SMC6 complex localization factor protein 1Q9BQI6 (reviewed: Q9BQI6)

Alternative names: Ankyrin repeat domain-containing protein 32, BRCT domain-containing protein 1, Smc5/6 localization factor 1

All UniProt accessions (3): D6RED9, Q9BQI6, H0YBU1

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance. The SLF1-SLF2 complex acts to link RAD18 with the SMC5-SMC6 complex at replication-coupled interstrand cross-links (ICL) and DNA double-strand breaks (DSBs) sites on chromatin during DNA repair in response to stalled replication forks. Promotes the recruitment of SLF2 and the SMC5-SMC6 complex to DNA lesions.

Subunit / interactions. Interacts (via N-terminus) with SLF2; this interaction links RAD18 to the SMC5-SMC6 complex. Interacts (via BRCT domains) with RAD18; this interaction occurs in a SLF2-independent manner. Interacts with SMC6. Interacts (via BRCT domains) with RAD18 (via C-terminus and phosphorylated form); this interaction is required for efficient repair of UV-induced DNA damage.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Domain organisation. BRCT domains are necessary for its targeting to ionizing radiation-induced nuclear foci.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BQI6-11yes
Q9BQI6-22

RefSeq proteins (1): NP_115666* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001357BRCT_domDomain
IPR002110Ankyrin_rptRepeat
IPR036420BRCT_dom_sfHomologous_superfamily
IPR036770Ankyrin_rpt-contain_sfHomologous_superfamily
IPR042479Slf1Family
IPR049935BRCT_SLF1Domain
IPR057595TopB1_SLF1_BRCTDomain

Pfam: PF12796, PF16770, PF23294

UniProt features (42 total): helix 18, strand 7, sequence conflict 5, repeat 3, domain 2, splice variant 2, chain 1, sequence variant 1, turn 1, region of interest 1, cross-link 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
8PEFX-RAY DIFFRACTION1.28
8IR4X-RAY DIFFRACTION1.62
8IR2X-RAY DIFFRACTION1.75

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BQI6-F169.350.25

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 (1): 931

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 183 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_CHROMOSOME_ORGANIZATION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_TELOMERE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_DNA_REPAIR, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_REGULATION_OF_TELOMERE_MAINTENANCE, GOBP_PEPTIDYL_LYSINE_MODIFICATION, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, GOBP_SISTER_CHROMATID_COHESION, GOBP_PROTEIN_LOCALIZATION_TO_CHROMOSOME, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (10): double-strand break repair via homologous recombination (GO:0000724), DNA damage response (GO:0006974), protein sumoylation (GO:0016925), positive regulation of protein-containing complex assembly (GO:0031334), regulation of telomere maintenance (GO:0032204), positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184), chromatin looping (GO:0140588), protein localization to site of double-strand break (GO:1990166), positive regulation of double-strand break repair (GO:2000781), DNA repair (GO:0006281)

GO Molecular Function (3): ubiquitin protein ligase binding (GO:0031625), protein-containing complex binding (GO:0044877), protein binding (GO:0005515)

GO Cellular Component (11): chromosome, telomeric region (GO:0000781), nucleosome (GO:0000786), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), centrosome (GO:0005813), Smc5-Smc6 complex (GO:0030915), site of double-strand break (GO:0035861), nuclear inclusion body (GO:0042405), chromosome (GO:0005694), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
double-strand break repair2
binding2
cellular anatomical structure2
intracellular membraneless organelle2
recombinational repair1
cellular response to stress1
peptidyl-lysine modification1
protein modification by small protein conjugation1
regulation of protein-containing complex assembly1
positive regulation of cellular component biogenesis1
positive regulation of cellular component organization1
protein-containing complex assembly1
telomere maintenance1
regulation of chromosome organization1
regulation of DNA metabolic process1
maintenance of mitotic sister chromatid cohesion1
positive regulation of maintenance of sister chromatid cohesion1
regulation of maintenance of mitotic sister chromatid cohesion1
chromatin organization1
protein localization to chromosome1
positive regulation of DNA repair1
regulation of double-strand break repair1
DNA metabolic process1
DNA damage response1
ubiquitin-like protein ligase binding1
chromosomal region1
chromatin1
protein-DNA complex1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
centriole1
microtubule organizing center1
condensed chromosome1
SUMO ligase complex1
site of DNA damage1
nucleus1
inclusion body1

Protein interactions and networks

STRING

2925 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SLF1SLF2Q8IX21987
SLF1RAD18Q9NS91784
SLF1SMC5Q8IY18772
SLF1NSMCE1Q8WV22593
SLF1ARB2AQ8WUF8572
SLF1RNF168Q8IYW5571
SLF1TP53BP1Q12888530
SLF1PAXIP1Q6ZW49525
SLF1MCTP1Q6DN14524
SLF1RNF169Q8NCN4515
SLF1NSMCE2Q96MF7507
SLF1SMC6Q96SB8498
SLF1MDC1Q14676493
SLF1NSMCE3Q96MG7465
SLF1HLTFQ14527460

IntAct

25 interactions, top by confidence:

ABTypeScore
SLF2SLF1psi-mi:“MI:0915”(physical association)0.780
SLF1SLF2psi-mi:“MI:0914”(association)0.780
NFKB1NFKBIEpsi-mi:“MI:2364”(proximity)0.600
MAGEA10POTEFpsi-mi:“MI:0914”(association)0.530
SLF1PDIA6psi-mi:“MI:0915”(physical association)0.400
UBTFSLF1psi-mi:“MI:0915”(physical association)0.400
PARD6BPARD3psi-mi:“MI:0914”(association)0.350
SMC6IFT88psi-mi:“MI:0914”(association)0.350
SLF2GCFC2psi-mi:“MI:0914”(association)0.350
RAD18SRGAP3psi-mi:“MI:0914”(association)0.350
NFKB1NFKB1psi-mi:“MI:0914”(association)0.350
RAD18H2AC4psi-mi:“MI:0914”(association)0.350
PIPSLC1orf226psi-mi:“MI:0914”(association)0.350
FTLSH3PXD2Bpsi-mi:“MI:0914”(association)0.350
SLF1CD8Apsi-mi:“MI:0914”(association)0.350
FTLpsi-mi:“MI:0914”(association)0.350
MAGEA10KANSL1Lpsi-mi:“MI:0914”(association)0.350
BRCA1SMCHD1psi-mi:“MI:2364”(proximity)0.270

BioGRID (36): ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Two-hybrid), ANKRD32 (Affinity Capture-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Proximity Label-MS), ANKRD32 (Affinity Capture-MS), ANKRD32 (Proximity Label-MS), ANKRD32 (Proximity Label-MS), ANKRD32 (Negative Genetic)

ESM2 similar proteins: A0A0A6YYL3, A0JP26, A2A2Z9, A2RUR9, A6NC57, A6NI47, A6QR20, A8MYB1, A9JSR5, A9ZSY0, B2RU33, B7ZQJ9, F1M5M3, H3BUK9, O15050, P51954, P98182, Q19UN5, Q4UJ75, Q501X2, Q5CZ79, Q5DW34, Q5SQ80, Q5TYW2, Q5VUR7, Q66HB6, Q6NSI1, Q6S545, Q6S5H5, Q6S8J7, Q71S21, Q7TPV2, Q7TSC3, Q7ZT11, Q80X59, Q811D2, Q86Y13, Q86YR6, Q8IVF6, Q8IYA2

Diamond homologs: A2AQH4, A2AS55, A6NGH8, A6QR20, O14974, Q2T9W8, Q499M5, Q5H9F3, Q641X1, Q6P6B7, Q6W2J9, Q86WC6, Q8CGN4, Q9BQI6, Q9D119, Q9UU77, Q9XZC0, A4II29, A5WVX9, B4E2M5, D3Z7P3, E9PTT0, G5EGA3, O83515, O94925, P13264, Q01317, Q15653, Q21920, Q3SX45, Q3U0L2, Q4FE45, Q4JHE0, Q502K3, Q54HW1, Q5U5A6, Q6NSI1, Q6NY19, Q7T3Y0, Q7Z6K4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance142
Likely benign13
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

4478 predictions. Top by Δscore:

VariantEffectΔscore
5:94628795:T:Gacceptor_gain1.0000
5:94628799:T:TAacceptor_gain1.0000
5:94628802:A:AGacceptor_gain1.0000
5:94628802:ATTT:Aacceptor_gain1.0000
5:94628803:T:Gacceptor_gain1.0000
5:94628805:T:TAacceptor_gain1.0000
5:94628806:GTTAG:Gacceptor_loss1.0000
5:94628807:TTAGA:Tacceptor_loss1.0000
5:94628808:TAGAT:Tacceptor_loss1.0000
5:94628809:A:AGacceptor_gain1.0000
5:94628809:A:Tacceptor_loss1.0000
5:94628810:G:GAacceptor_gain1.0000
5:94628871:G:GTdonor_gain1.0000
5:94628920:GTGAG:Gdonor_gain1.0000
5:94628921:TGAGG:Tdonor_loss1.0000
5:94628922:GAGGT:Gdonor_loss1.0000
5:94628923:AGGTA:Adonor_loss1.0000
5:94628924:GGTA:Gdonor_loss1.0000
5:94628925:G:GCdonor_loss1.0000
5:94628926:T:Gdonor_loss1.0000
5:94629090:A:AGacceptor_gain1.0000
5:94629091:G:GGacceptor_gain1.0000
5:94630499:CTAGG:Cacceptor_loss1.0000
5:94630500:TA:Tacceptor_loss1.0000
5:94630501:A:Cacceptor_loss1.0000
5:94630502:G:GCacceptor_loss1.0000
5:94630502:GGAAA:Gacceptor_gain1.0000
5:94630694:A:Tdonor_gain1.0000
5:94630719:A:Gdonor_gain1.0000
5:94630725:G:GTdonor_gain1.0000

AlphaMissense

7029 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:94630508:T:AW66R0.999
5:94630508:T:CW66R0.999
5:94692085:T:AW842R0.999
5:94692085:T:CW842R0.999
5:94692092:C:AP844H0.999
5:94629114:T:CL46P0.998
5:94630556:T:AW82R0.998
5:94630556:T:CW82R0.998
5:94691587:T:CC815R0.998
5:94691589:C:GC815W0.998
5:94691656:G:CD838H0.998
5:94692074:A:CD838A0.998
5:94692074:A:TD838V0.998
5:94692087:G:CW842C0.998
5:94692087:G:TW842C0.998
5:94692092:C:GP844R0.998
5:94692103:G:CA848P0.998
5:94692107:G:AC849Y0.998
5:94692108:T:GC849W0.998
5:94692116:G:TG852V0.998
5:94692131:T:AV857D0.998
5:94692205:G:CA882P0.998
5:94692209:T:CL883P0.998
5:94692242:T:CL894P0.998
5:94630580:T:AW90R0.997
5:94630580:T:CW90R0.997
5:94630643:T:AW111R0.997
5:94630643:T:CW111R0.997
5:94630691:T:AW127R0.997
5:94630691:T:CW127R0.997

dbSNP variants (sampled 300 via entrez): RS1000017444 (5:94684538 A>C,G), RS1000024937 (5:94651247 T>C), RS1000040914 (5:94643149 C>A), RS1000088048 (5:94692683 A>G,T), RS1000129047 (5:94654791 G>C), RS1000153765 (5:94627979 C>T), RS1000180376 (5:94671677 T>C), RS1000199076 (5:94678357 G>T), RS1000240404 (5:94690705 A>C,G), RS1000310182 (5:94668880 G>C), RS1000353418 (5:94624829 A>G), RS1000359851 (5:94681637 ACCCTCCC>A), RS1000440133 (5:94675099 T>G), RS1000465751 (5:94630579 A>G), RS1000475474 (5:94633876 G>C,T)

Disease associations

OMIM: gene MIM:618467 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST010701_40Cortical surface area (MOSTest)9.000000e-23
GCST010702_25Subcortical volume (MOSTest)4.000000e-39
GCST010703_194Brain morphology (MOSTest)9.000000e-11
GCST90093325_9Language functional connectivity7.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement
EFO:0007797language measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression5
trichostatin Aaffects cotreatment, decreases expression3
Cyclosporineaffects expression, decreases expression3
Resveratrolaffects cotreatment, increases expression2
Cisplatindecreases expression, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tetrachlorodibenzodioxindecreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Aflatoxin B1affects expression, decreases methylation2
TAK-243increases sumoylation1
aminomethylphosphonic acid (AMPA)increases expression1
dicrotophosdecreases expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteaffects methylation1
potassium chromate(VI)decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneincreases expression, affects cotreatment1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangdecreases expression1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Acetaminophenincreases expression1
Glyphosateincreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicaffects methylation1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.