SSBP4

Summary

SSBP4 (single stranded DNA binding protein 4, HGNC:15676) is a protein-coding gene on chromosome 19p13.11, encoding Single-stranded DNA-binding protein 4 (Q9BWG4).

Predicted to enable single-stranded DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in membrane. Predicted to be active in nucleus.

Source: NCBI Gene 170463 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 80 total
• MANE Select transcript: NM_032627

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15676
Approved symbol	SSBP4
Name	single stranded DNA binding protein 4
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000130511
Ensembl biotype	protein_coding
OMIM	607391
Entrez	170463

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 16 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000270061, ENST00000348495, ENST00000593641, ENST00000597724, ENST00000598159, ENST00000599699, ENST00000600244, ENST00000600628, ENST00000601357, ENST00000601444, ENST00000601614, ENST00000601919, ENST00000602088, ENST00000607020, ENST00000625926, ENST00000867041, ENST00000867042, ENST00000915352, ENST00000915353, ENST00000915354, ENST00000964016, ENST00000964017, ENST00000964018

RefSeq mRNA: 2 — MANE Select: NM_032627 NM_001009998, NM_032627

CCDS: CCDS12378, CCDS32960

Canonical transcript exons

ENST00000270061 — 18 exons

Exon	Start	End
ENSE00000895843	18433710	18433817
ENSE00003140945	18419398	18419707
ENSE00003476300	18433585	18433613
ENSE00003696354	18432829	18432883
ENSE00003697415	18433135	18433213
ENSE00003698780	18432973	18433043
ENSE00003699510	18432000	18432070
ENSE00003700553	18431793	18431862
ENSE00003700960	18432700	18432735
ENSE00003702231	18432559	18432604
ENSE00003702639	18430841	18430930
ENSE00003703150	18434217	18434562
ENSE00003703384	18427898	18427982
ENSE00003705156	18431647	18431706
ENSE00003706442	18427752	18427813
ENSE00003706557	18427351	18427423
ENSE00003707362	18431353	18431418
ENSE00003789942	18432147	18432214

Expression profiles

Bgee: expression breadth ubiquitous, 240 present calls, max score 99.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.4530 / max 144.3813, expressed in 1809 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174662	12.2929	1792
174670	2.0911	702
174663	1.3859	878
174671	0.4730	185
174661	0.4096	187
174660	0.3884	189
174659	0.1724	74
174666	0.0929	46
174658	0.0664	26
174667	0.0313	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.57	gold quality
adenohypophysis	UBERON:0002196	98.92	gold quality
granulocyte	CL:0000094	98.87	gold quality
pituitary gland	UBERON:0000007	98.34	gold quality
endocervix	UBERON:0000458	98.21	gold quality
left uterine tube	UBERON:0001303	98.12	gold quality
right frontal lobe	UBERON:0002810	98.03	gold quality
caudate nucleus	UBERON:0001873	98.01	gold quality
nucleus accumbens	UBERON:0001882	98.00	gold quality
body of uterus	UBERON:0009853	97.86	gold quality
right ovary	UBERON:0002118	97.85	gold quality
putamen	UBERON:0001874	97.84	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.71	gold quality
anterior cingulate cortex	UBERON:0009835	97.56	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.55	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.55	gold quality
left ovary	UBERON:0002119	97.53	gold quality
cerebellar hemisphere	UBERON:0002245	97.35	gold quality
cortical plate	UBERON:0005343	97.33	gold quality
cerebellar cortex	UBERON:0002129	97.28	gold quality
amygdala	UBERON:0001876	96.92	gold quality
right coronary artery	UBERON:0001625	96.75	gold quality
prefrontal cortex	UBERON:0000451	96.65	gold quality
ectocervix	UBERON:0012249	96.59	gold quality
apex of heart	UBERON:0002098	96.41	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.28	gold quality
nerve	UBERON:0001021	96.27	gold quality
tibial nerve	UBERON:0001323	96.27	gold quality
cerebellum	UBERON:0002037	96.22	gold quality
spleen	UBERON:0002106	96.21	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.96
E-MTAB-7606	no	295.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting SSBP4, 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-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-224-3P	98.91	68.42	1815
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-2115-5P	98.66	68.07	1191
HSA-MIR-326	98.25	66.44	1565
HSA-MIR-5007-5P	97.95	64.71	614
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-4653-5P	97.22	67.72	1429

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	ssbp4	ENSDARG00000056483
danio_rerio	SSBP4	ENSDARG00000056490
mus_musculus	Ssbp4	ENSMUSG00000070003
rattus_norvegicus	Ssbp4	ENSRNOG00000019698
drosophila_melanogaster	Ssdp	FBGN0011481
caenorhabditis_elegans		WBGENE00012990
caenorhabditis_elegans		WBGENE00013152

Paralogs (2): SSBP2 (ENSG00000145687), SSBP3 (ENSG00000157216)

Protein

Protein identifiers

Single-stranded DNA-binding protein 4 — Q9BWG4 (reviewed: Q9BWG4)

All UniProt accessions (8): Q9BWG4, M0R338, U3KPY3, U3KQ46, U3KQ98, U3KQN6, U3KQP2, V9GYB2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BWG4-1	1	yes
Q9BWG4-2	2

RefSeq proteins (2): NP_001009998, NP_116016* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006594	LisH	Conserved_site
IPR008116	SSDP_DNA-bd	Family

Pfam: PF04503

UniProt features (10 total): modified residue 3, region of interest 2, compositionally biased region 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7OBX	X-RAY DIFFRACTION	1.8
7OBY	X-RAY DIFFRACTION	2.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWG4-F1	55.25	0.14

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 (3): 1, 341, 355

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 167 (showing top): BENPORATH_ES_WITH_H3K27ME3, MODULE_255, AREB6_03, MODULE_317, GGGTGGRR_PAX4_03, LIAO_METASTASIS, MORI_PRE_BI_LYMPHOCYTE_UP, PU1_Q6, RYTTCCTG_ETS2_B, BASAKI_YBX1_TARGETS_DN, RGAGGAARY_PU1_Q6, RIGGI_EWING_SARCOMA_PROGENITOR_UP, GOMF_SINGLE_STRANDED_DNA_BINDING, AHR_Q5, MARSON_BOUND_BY_FOXP3_STIMULATED

GO Biological Process (1): positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (3): single-stranded DNA binding (GO:0003697), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
DNA binding	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

528 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSBP4	LDB1	Q86U70	505
SSBP4	LRRC25	Q8N386	495
SSBP4	INIP	Q9NRY2	470
SSBP4	SSBP1	Q04837	464
SSBP4	LDB2	O43679	447
SSBP4	MRPL34	Q9BQ48	395
SSBP4	INTS3	Q68E01	385
SSBP4	SNX32	Q86XE0	349
SSBP4	PGPEP1	Q9NXJ5	331
SSBP4	ELL	P55199	324
SSBP4	PPP1R2C	O14990	323
SSBP4	SPANXN1	Q5VSR9	322
SSBP4	DCLRE1B	Q9H816	318
SSBP4	IQCN	Q9H0B3	317
SSBP4	SPATA25	Q9BR10	314

IntAct

75 interactions, top by confidence:

A	B	Type	Score
LMO1	ZBTB43	psi-mi:“MI:0914”(association)	0.830
SSBP3	LMX1B	psi-mi:“MI:0914”(association)	0.740
PYGO1	BCL9	psi-mi:“MI:0914”(association)	0.700
PIN1	SSBP4	psi-mi:“MI:0915”(physical association)	0.670
SSBP4	IL36RN	psi-mi:“MI:0915”(physical association)	0.670
LDB1	SSBP4	psi-mi:“MI:0915”(physical association)	0.670
IL36RN	SSBP4	psi-mi:“MI:0915”(physical association)	0.670
ISL1	SSBP4	psi-mi:“MI:0915”(physical association)	0.660
LDB1	SSBP4	psi-mi:“MI:0915”(physical association)	0.660
MYO15B	SSBP4	psi-mi:“MI:0915”(physical association)	0.560
PIK3R3	SSBP4	psi-mi:“MI:0915”(physical association)	0.560
SSBP4	SPG21	psi-mi:“MI:0915”(physical association)	0.560
LDB2	SSBP4	psi-mi:“MI:0915”(physical association)	0.550
LMO3	ZBTB43	psi-mi:“MI:0914”(association)	0.550
SSBP4	LDB2	psi-mi:“MI:0914”(association)	0.550
SSBP2	CLEC18A	psi-mi:“MI:0914”(association)	0.530
SSBP4	GM2A	psi-mi:“MI:0914”(association)	0.530
PICK1	ILVBL	psi-mi:“MI:0914”(association)	0.530
LHX4	THAP12	psi-mi:“MI:0914”(association)	0.530
SSBP4	LMX1B	psi-mi:“MI:0914”(association)	0.530
TFAP2B	SSBP4	psi-mi:“MI:0915”(physical association)	0.370
NUDCD1	TUBAL3	psi-mi:“MI:0914”(association)	0.350
NUDCD1	DNAJB2	psi-mi:“MI:0914”(association)	0.350
LMX1B	POTEF	psi-mi:“MI:0914”(association)	0.350
LMO2	APBB1	psi-mi:“MI:0914”(association)	0.350
IDI2	LMX1B	psi-mi:“MI:0914”(association)	0.350

BioGRID (113): SSBP4 (Affinity Capture-RNA), SSBP4 (Affinity Capture-MS), SSBP4 (Affinity Capture-MS), SSBP4 (Affinity Capture-MS), LDB1 (Affinity Capture-MS), LHX1 (Affinity Capture-MS), MBNL1 (Affinity Capture-MS), ISL2 (Affinity Capture-MS), ISL1 (Affinity Capture-MS), SSBP3 (Affinity Capture-MS), LHX8 (Affinity Capture-MS), LMO4 (Affinity Capture-MS), GM2A (Affinity Capture-MS), LHX4 (Affinity Capture-MS), SSBP4 (Affinity Capture-MS)

ESM2 similar proteins: A1YFU7, A2AJK6, A2BH40, B2RWS6, D3YWE6, E9Q4N7, M9NEY8, O00512, O14497, O35126, O42368, O43365, O57401, P02831, P02833, P22810, P23441, P23512, P25822, P32182, P34545, P35582, P35583, P43698, P43699, P50220, P50901, P54258, P54259, P54269, P55317, Q06A37, Q08DG7, Q08E31, Q09472, Q0VCT9, Q10571, Q1KKX7, Q24248, Q24645

Diamond homologs: B7FAS6, P81877, Q98948, Q9BWG4, Q9BWW4, Q9CYZ8, Q9D032, Q9R050, A0AUS0, A1CUD6, A6ZR64, A7RHG8, A7YY75, B2AEZ5, B3LRM5, B5VHN4, B6GZD3, B6HP56, B6QC06, B8N9H4, B9WD30, C0S902, C1BK83, C1GB49, C4JPW9, C7GS77, C8Z7C7, D5GBI7, O14186, O22212, O35828, O48847, O74184, P0CS38, P0CS39, P40068, P74598, P87314, Q05BV3, Q06440

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 58 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
Signaling by ROBO receptors	6	20.7×	1e-04
Regulation of expression of SLITs and ROBOs	6	11.5×	1e-03
Axon guidance	7	8.8×	1e-03
Nervous system development	7	8.3×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
neuron differentiation	11	20.4×	2e-09
axonogenesis	5	14.9×	1e-03
transcription by RNA polymerase II	7	9.1×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2360 predictions. Top by Δscore:

Variant	Effect	Δscore
19:18419705:GAA:G	donor_gain	1.0000
19:18419708:G:GG	donor_gain	1.0000
19:18427421:GAG:G	donor_gain	1.0000
19:18427422:AGGT:A	donor_loss	1.0000
19:18427424:G:GG	donor_gain	1.0000
19:18427424:GT:G	donor_loss	1.0000
19:18427425:T:A	donor_loss	1.0000
19:18427888:T:TA	acceptor_gain	1.0000
19:18427889:G:A	acceptor_gain	1.0000
19:18427893:CACA:C	acceptor_loss	1.0000
19:18427895:CA:C	acceptor_loss	1.0000
19:18427896:A:AG	acceptor_gain	1.0000
19:18427896:AGC:A	acceptor_gain	1.0000
19:18427897:G:GT	acceptor_gain	1.0000
19:18427897:GC:G	acceptor_gain	1.0000
19:18427897:GCG:G	acceptor_gain	1.0000
19:18427897:GCGT:G	acceptor_gain	1.0000
19:18427897:GCGTC:G	acceptor_gain	1.0000
19:18427977:GAC:G	donor_gain	1.0000
19:18427980:TAT:T	donor_gain	1.0000
19:18427982:TGTG:T	donor_loss	1.0000
19:18427983:G:GG	donor_gain	1.0000
19:18430828:C:A	acceptor_gain	1.0000
19:18430831:A:AG	acceptor_gain	1.0000
19:18430832:C:G	acceptor_gain	1.0000
19:18430840:GA:G	acceptor_gain	1.0000
19:18430926:TCCAG:T	donor_loss	1.0000
19:18430927:CCAGG:C	donor_loss	1.0000
19:18430928:CAGGT:C	donor_loss	1.0000
19:18430929:AGGTA:A	donor_loss	1.0000

AlphaMissense

2512 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:18427353:T:C	L21S	1.000
19:18427365:T:A	V25D	1.000
19:18427373:T:G	Y28D	1.000
19:18427377:T:C	L29P	1.000
19:18427380:T:C	L30P	1.000
19:18427404:C:A	A38D	1.000
19:18427412:T:C	F41L	1.000
19:18427413:T:C	F41S	1.000
19:18427413:T:G	F41C	1.000
19:18427414:C:A	F41L	1.000
19:18427414:C:G	F41L	1.000
19:18427416:T:C	L42P	1.000
19:18427758:T:A	W47R	1.000
19:18427758:T:C	W47R	1.000
19:18427794:T:C	F59L	1.000
19:18427795:T:C	F59S	1.000
19:18427796:C:A	F59L	1.000
19:18427796:C:G	F59L	1.000
19:18427806:T:A	W63R	1.000
19:18427806:T:C	W63R	1.000
19:18427809:T:A	W64R	1.000
19:18427809:T:C	W64R	1.000
19:18427902:T:C	F67L	1.000
19:18427903:T:C	F67S	1.000
19:18427904:C:A	F67L	1.000
19:18427904:C:G	F67L	1.000
19:18427905:T:A	W68R	1.000
19:18427905:T:C	W68R	1.000
19:18427907:G:C	W68C	1.000
19:18427907:G:T	W68C	1.000

dbSNP variants (sampled 300 via entrez): RS1000005251 (19:18405554 A>G), RS1000114419 (19:18427552 G>A), RS1000123391 (19:18404988 C>A,G,T), RS1000159466 (19:18411001 G>A), RS1000183561 (19:18424730 G>A,C,T), RS1000188673 (19:18426364 G>A), RS1000197673 (19:18421901 T>A), RS1000212910 (19:18424888 G>A), RS1000219679 (19:18426102 C>T), RS1000247028 (19:18425212 A>G,T), RS1000493293 (19:18429624 GGA>G), RS1000521980 (19:18409587 G>C,T), RS1000697465 (19:18414553 G>A), RS1000777689 (19:18429474 G>GC,GT), RS1000803071 (19:18420612 C>A)

Disease associations

OMIM: gene MIM:607391 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST001937_26	Breast cancer	5.000000e-15
GCST004625_212	Monocyte count	2.000000e-10
GCST005752_105	Systemic lupus erythematosus	1.000000e-08
GCST007400_25	Systemic lupus erythematosus	7.000000e-07
GCST007511_22	Alzheimer’s disease (late onset)	2.000000e-06
GCST008759_26	Intake of total sugars	2.000000e-06
GCST011096_19	Systemic lupus erythematosus	1.000000e-10
GCST011097_3	Systemic lupus erythematosus	2.000000e-06
GCST011956_115	Systemic lupus erythematosus	4.000000e-12
GCST90002379_197	Basophil count	9.000000e-11

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005091	monocyte count
EFO:1001870	late-onset Alzheimers disease
EFO:0010158	sugar consumption measurement
EFO:0005090	basophil count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	5
sodium arsenite	decreases expression, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	decreases expression	2
Cadmium Chloride	decreases expression	2
FR900359	increases phosphorylation	1
methylmercuric chloride	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	decreases expression	1
aflatoxin B2	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
eprenetapopt	affects expression, affects reaction	1
jinfukang	increases expression	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases expression	1
Catechin	affects cotreatment, decreases expression	1
Copper	decreases expression, affects binding	1
Hydralazine	affects cotreatment, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Aflatoxin B1	increases methylation	1
Fenretinide	decreases expression	1
Antirheumatic Agents	increases expression	1

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B3IA	Abcam HEK293T SSBP4 KO	Transformed cell line	Female
CVCL_TQ51	HAP1 SSBP4 (-) 1	Cancer cell line	Male
CVCL_XT88	HAP1 SSBP4 (-) 2	Cancer cell line	Male
CVCL_XT89	HAP1 SSBP4 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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