SLFNL1

Summary

SLFNL1 (schlafen like 1, HGNC:26313) is a protein-coding gene on chromosome 1p34.2, encoding Schlafen-like protein 1 (Q499Z3).

Predicted to enable ATP binding activity.

Source: NCBI Gene 200172 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 111 total
• MANE Select transcript: NM_144990

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26313
Approved symbol	SLFNL1
Name	schlafen like 1
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23878
Ensembl gene	ENSG00000171790
Ensembl biotype	protein_coding
Entrez	200172

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000302946, ENST00000359345, ENST00000372611, ENST00000372613, ENST00000439569, ENST00000688905, ENST00000689703, ENST00000690672, ENST00000693284, ENST00000693533, ENST00000895831, ENST00000895832, ENST00000943707, ENST00000943708

RefSeq mRNA: 5 — MANE Select: NM_144990 NM_001168247, NM_001300859, NM_001377532, NM_001394331, NM_144990

CCDS: CCDS460, CCDS72766, CCDS90925

Canonical transcript exons

ENST00000302946 — 6 exons

Exon	Start	End
ENSE00001122910	41017234	41017377
ENSE00001122916	41017635	41018156
ENSE00001213172	41015597	41016228
ENSE00001213181	41020226	41020778
ENSE00003924297	41020864	41020870
ENSE00003933547	41021623	41021725

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 95.85.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0945 / max 82.0975, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11941	0.0878	4
11942	0.0068	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	95.85	gold quality
left testis	UBERON:0004533	94.13	gold quality
right testis	UBERON:0004534	93.79	gold quality
testis	UBERON:0000473	90.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.61	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.27	gold quality
adult organism	UBERON:0007023	76.96	gold quality
epithelium of nasopharynx	UBERON:0001951	71.25	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	69.19	gold quality
biceps brachii	UBERON:0001507	67.34	gold quality
cerebellar vermis	UBERON:0004720	67.08	gold quality
parotid gland	UBERON:0001831	65.78	gold quality
gingival epithelium	UBERON:0001949	65.34	gold quality
oocyte	CL:0000023	64.83	gold quality
lateral globus pallidus	UBERON:0002476	64.62	gold quality
stromal cell of endometrium	CL:0002255	64.34	gold quality
mucosa of paranasal sinus	UBERON:0005030	63.96	gold quality
quadriceps femoris	UBERON:0001377	63.75	gold quality
gingiva	UBERON:0001828	63.36	gold quality
secondary oocyte	CL:0000655	63.26	gold quality
vastus lateralis	UBERON:0001379	62.93	gold quality
superficial temporal artery	UBERON:0001614	62.73	gold quality
buccal mucosa cell	CL:0002336	62.51	gold quality
tonsil	UBERON:0002372	62.46	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	62.38	gold quality
Brodmann (1909) area 23	UBERON:0013554	62.36	gold quality
bone marrow cell	CL:0002092	61.93	gold quality
substantia nigra pars reticulata	UBERON:0001966	61.76	gold quality
thymus	UBERON:0002370	61.74	gold quality
liver	UBERON:0002107	61.53	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.30

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting SLFNL1, 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-4766-5P	99.75	69.23	2662
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-7843-3P	98.31	67.94	803
HSA-MIR-4704-3P	98.28	69.33	1300
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-188-5P	97.89	67.01	756
HSA-MIR-6866-3P	97.38	66.94	748
HSA-MIR-3974	96.56	66.22	928
HSA-MIR-6823-5P	96.26	65.69	919
HSA-MIR-6874-5P	95.73	64.94	545
HSA-MIR-6734-5P	95.70	65.56	950
HSA-MIR-193A-5P	95.70	65.33	613
HSA-MIR-3162-5P	95.67	67.53	794

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slfnl1	ENSMUSG00000047518
rattus_norvegicus	Slfnl1	ENSRNOG00000032183

Paralogs (6): SLFN13 (ENSG00000154760), SLFN5 (ENSG00000166750), SLFN12 (ENSG00000172123), SLFN11 (ENSG00000172716), SLFN12L (ENSG00000205045), SLFN14 (ENSG00000236320)

Protein

Protein identifiers

Schlafen-like protein 1 — Q499Z3 (reviewed: Q499Z3)

All UniProt accessions (6): Q499Z3, A0A140VJU6, A0A8I5KV89, A0A8I5KXE0, A0A8I5KYI0, A0A8I5KYM2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the Schlafen family. Subgroup I subfamily.

Isoforms (4)

UniProt ID	Names	Canonical?
Q499Z3-1	1	yes
Q499Z3-2	2
Q499Z3-3	3
Q499Z3-4	4

RefSeq proteins (5): NP_001161719, NP_001287788, NP_001364461, NP_001381260, NP_659427* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007421	Schlafen_AlbA_2_dom	Domain
IPR029684	Schlafen	Family
IPR038461	Schlafen_AlbA_2_dom_sf	Homologous_superfamily

Pfam: PF04326

UniProt features (16 total): splice variant 4, sequence variant 3, region of interest 2, sequence conflict 2, compositionally biased region 2, chain 1, coiled-coil region 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q499Z3-F1	72.65	0.35

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (1): 261–268

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): chr1p34, GOMF_ADENYL_NUCLEOTIDE_BINDING, SETD7_TARGET_GENES, MIR4766_5P, GSE11864_CSF1_IFNG_VS_CSF1_PAM3CYS_IN_MAC_DN, GSE11924_TFH_VS_TH1_CD4_TCELL_DN, GSE11924_TH1_VS_TH17_CD4_TCELL_UP, MIR3974, GSE15659_NAIVE_CD4_TCELL_VS_RESTING_TREG_DN, GSE15659_NAIVE_CD4_TCELL_VS_ACTIVATED_TREG_DN, GSE15659_CD45RA_NEG_CD4_TCELL_VS_RESTING_TREG_DN, GSE15659_CD45RA_NEG_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_DN, GSE15659_RESTING_TREG_VS_NONSUPPRESSIVE_TCELL_DN, GSE15659_RESTING_VS_ACTIVATED_TREG_DN, ZNF41_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): ATP binding (GO:0005524), nucleotide binding (GO:0000166)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1

Protein interactions and networks

STRING

1880 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLFNL1	STPG3	Q8N7X2	694
SLFNL1	TEX36	Q5VZQ5	666
SLFNL1	GLT6D1	Q7Z4J2	617
SLFNL1	FAM187B	Q17R55	606
SLFNL1	SMKR1	H3BMG3	602
SLFNL1	EVPLL	A8MZ36	572
SLFNL1	SPPL2C	Q8IUH8	547
SLFNL1	ZNF587B	E7ETH6	505
SLFNL1	C9orf152	Q5JTZ5	474
SLFNL1	CT47B1	P0C2W7	471
SLFNL1	PRSS58	Q8IYP2	470
SLFNL1	CA11	O75493	449
SLFNL1	SLFN12L	Q6IEE8	392
SLFNL1	KLHL10	Q6JEL2	378
SLFNL1	OXCT2	Q9BYC2	370

IntAct

0 interactions, top by confidence:

BioGRID (3): SLFNL1 (Affinity Capture-RNA), SLFNL1 (Protein-peptide), APP (Reconstituted Complex)

ESM2 similar proteins: A0A1B0GTW7, A0A1D5NSK0, A0A1L8HYT7, A0A286YEC0, D3ZT86, D3ZWJ9, D4A929, F8W3R9, G7PWZ3, I6M4H4, O08852, O43157, O43278, O75074, O88204, P17813, P49000, P59383, Q04912, Q17R55, Q499Z3, Q4R3B7, Q4TUC0, Q5ND34, Q62190, Q63961, Q6AXX1, Q76MJ5, Q7TN88, Q7TQH7, Q7Z442, Q7Z4F1, Q80W87, Q80YN4, Q866Y3, Q86VZ4, Q8BHW9, Q8BMN4, Q8BYI8, Q8BZT7

Diamond homologs: Q499Z3, Q4R3B7, Q6AXX1, Q8BHW9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	99
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1031 predictions. Top by Δscore:

Variant	Effect	Δscore
1:41016224:CACCT:C	acceptor_gain	1.0000
1:41020225:CCT:C	donor_gain	1.0000
1:41016226:CCTCT:C	acceptor_loss	0.9900
1:41016227:CT:C	acceptor_gain	0.9900
1:41016227:CTCTG:C	acceptor_loss	0.9900
1:41016229:C:CA	acceptor_loss	0.9900
1:41016229:C:CC	acceptor_gain	0.9900
1:41016230:T:A	acceptor_loss	0.9900
1:41017228:CCGTA:C	donor_loss	0.9900
1:41017229:CGTA:C	donor_loss	0.9900
1:41017230:GTACC:G	donor_loss	0.9900
1:41017231:TA:T	donor_loss	0.9900
1:41017233:C:CG	donor_loss	0.9900
1:41020222:TTAC:T	donor_loss	0.9900
1:41020223:TACCT:T	donor_loss	0.9900
1:41020224:A:AC	donor_gain	0.9900
1:41020224:AC:A	donor_gain	0.9900
1:41020225:C:CC	donor_gain	0.9900
1:41020225:CC:C	donor_gain	0.9900
1:41020225:CCTCT:C	donor_gain	0.9900
1:41016225:ACCT:A	acceptor_gain	0.9800
1:41016226:CCTC:C	acceptor_gain	0.9800
1:41017236:G:A	donor_gain	0.9800
1:41020224:ACCT:A	donor_gain	0.9800
1:41020225:CCTC:C	donor_gain	0.9800
1:41017232:ACCTG:A	donor_gain	0.9700
1:41017233:CCTGC:C	donor_gain	0.9700
1:41017629:GCTCA:G	donor_loss	0.9700
1:41017631:TCA:T	donor_loss	0.9700
1:41017632:CACCT:C	donor_loss	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000168038 (1:41021273 C>A,G), RS1001209020 (1:41022148 G>T), RS1001224468 (1:41021578 G>A), RS1001385193 (1:41015248 C>T), RS1002238206 (1:41022716 C>G), RS1002877588 (1:41018964 C>A,G,T), RS1002944678 (1:41019074 C>T), RS1003271014 (1:41023668 C>T), RS1003781424 (1:41023153 A>G), RS1004290777 (1:41018428 A>G), RS1004343199 (1:41018688 T>C), RS1004423573 (1:41017438 T>C), RS1004521114 (1:41021627 A>G), RS1004616352 (1:41022848 T>C), RS1005060227 (1:41021765 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST011771_2	Rapid response to perioperative phenylephrine (change in mean arterial pressure)	6.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006943	blood pressure change measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, increases expression	2
quercitrin	increases expression	1
perfluorooctanoic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Diazinon	decreases methylation	1
Nickel	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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