SOBP

Summary

SOBP (sine oculis binding protein homolog, HGNC:29256) is a protein-coding gene on chromosome 6q21, encoding Sine oculis-binding protein homolog (A7XYQ1). Implicated in development of the cochlea.

The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability.

Source: NCBI Gene 55084 — RefSeq curated summary.

At a glance

• Gene–disease (curated): intellectual disability, anterior maxillary protrusion, and strabismus (Supportive, GenCC) — +1 more curated relationship
• GWAS associations: 2
• Clinical variants (ClinVar): 200 total
• Phenotypes (HPO): 17
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_018013

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29256
Approved symbol	SOBP
Name	sine oculis binding protein homolog
Location	6q21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10159
Ensembl gene	ENSG00000112320
Ensembl biotype	protein_coding
OMIM	613667
Entrez	55084

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000317357, ENST00000477448, ENST00000494935, ENST00000618129, ENST00000911405, ENST00000911406, ENST00000911407, ENST00000954033

RefSeq mRNA: 1 — MANE Select: NM_018013 NM_018013

CCDS: CCDS43488

Canonical transcript exons

ENST00000317357 — 7 exons

Exon	Start	End
ENSE00001217811	107587080	107587175
ENSE00001448636	107658207	107661306
ENSE00001448638	107633514	107635469
ENSE00001913708	107490117	107490712
ENSE00003492196	107533459	107533610
ENSE00003648860	107506242	107506427
ENSE00003675879	107503657	107503795

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 99.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.9157 / max 487.8266, expressed in 1238 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
69158	9.8581	1137
69156	0.8786	421
69160	0.7833	309
69162	0.3448	125
69157	0.3301	157
69159	0.2462	138
69155	0.1828	87
69169	0.1511	68
69161	0.1408	71

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	99.56	gold quality
middle temporal gyrus	UBERON:0002771	99.39	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.28	gold quality
tibia	UBERON:0000979	99.24	gold quality
entorhinal cortex	UBERON:0002728	97.89	gold quality
Brodmann (1909) area 46	UBERON:0006483	97.78	gold quality
cortical plate	UBERON:0005343	97.75	gold quality
cerebellar vermis	UBERON:0004720	97.41	gold quality
buccal mucosa cell	CL:0002336	97.31	gold quality
orbitofrontal cortex	UBERON:0004167	97.22	gold quality
postcentral gyrus	UBERON:0002581	97.19	gold quality
parietal lobe	UBERON:0001872	97.16	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	96.57	gold quality
inferior olivary complex	UBERON:0002127	96.00	gold quality
blood vessel layer	UBERON:0004797	95.82	gold quality
parotid gland	UBERON:0001831	95.74	gold quality
pigmented layer of retina	UBERON:0001782	95.72	gold quality
superior frontal gyrus	UBERON:0002661	95.57	gold quality
CA1 field of hippocampus	UBERON:0003881	95.30	gold quality
adult organism	UBERON:0007023	95.20	gold quality
cartilage tissue	UBERON:0002418	94.70	gold quality
occipital lobe	UBERON:0002021	94.55	gold quality
cranial nerve II	UBERON:0000941	94.49	gold quality
ventral tegmental area	UBERON:0002691	94.33	gold quality
pons	UBERON:0000988	94.25	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.06	gold quality
inferior vagus X ganglion	UBERON:0005363	94.05	gold quality
primary visual cortex	UBERON:0002436	93.83	gold quality
heart right ventricle	UBERON:0002080	93.82	gold quality
medulla oblongata	UBERON:0001896	93.78	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.90
E-MTAB-8060	no	31.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

208 targeting SOBP, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
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-551B-5P	99.96	71.28	3493
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-545-3P	99.95	70.74	2783
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-497-5P	99.92	71.83	2674

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

• This study shows mutated SOBP involvement in syndromic and nonsyndromic ID with psychosis in humans. (PMID:21035105)
• The intragenic exon rearrangements (IERs) involved in SOBP (6q21) exon 2 and 3 and AUTS2 (7q11.22) exon 2-4 were the molecular lesions specific to tumors and were frequently detected in non-Hodgkin B cell lymphoma (B-NHL) samples. These IERs constitute novel genetic alterations of B-NHL, which might be associated with tumorigenesis and be useful as genetic biological markers. (PMID:31686349)
• Identification of MEG8/miR-378d/SOBP axis as a novel regulatory network and associated with immune infiltrates in ovarian carcinoma by integrated bioinformatics analysis. (PMID:33742531)
• Novel circular RNA circSOBP governs amoeboid migration through the regulation of the miR-141-3p/MYPT1/p-MLC2 axis in prostate cancer. (PMID:33784000)
• circSOBP Inhibits Bladder Cancer Proliferation and Metastasis by Regulating the miR-200a-3p/PTEN Axis and Participating in the Immune Response. (PMID:37026617)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	sobpa	ENSDARG00000054253
mus_musculus	Sobp	ENSMUSG00000038248
rattus_norvegicus	Sobp	ENSRNOG00000000316
drosophila_melanogaster	Sobp	FBGN0033654

Paralogs (1): RAI2 (ENSG00000131831)

Protein

Protein identifiers

Sine oculis-binding protein homolog — A7XYQ1 (reviewed: A7XYQ1)

Alternative names: Jackson circler protein 1

All UniProt accessions (2): A7XYQ1, A0A0C4DGT7

UniProt curated annotations — full annotation on UniProt →

Function. Implicated in development of the cochlea.

Subunit / interactions. Interacts (via SIM domains) with SUMO1 and SUMO2.

Disease relevance. Impaired intellectual development, anterior maxillary protrusion, and strabismus (MRAMS) [MIM:613671] A syndrome characterized by severe intellectual disability, strabismus and dysmorphic features such as anterior maxillary protrusion with vertical maxillary excess, open bite and prominent crowded teeth. Some patients may lack dysmorphic features and manifest temporal lobe epilepsy and psychosis. Esotropia and amblyopia are present in some individuals. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the SOBP family.

RefSeq proteins (1): NP_060483* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010507	Znf_MYM	Domain
IPR026092	RAI2/SOBP	Family

Pfam: PF06467, PF15279

UniProt features (22 total): compositionally biased region 6, region of interest 5, zinc finger region 2, modified residue 2, sequence conflict 2, short sequence motif 2, chain 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A7XYQ1-F1	52.41	0.07

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): 629, 699, 677

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 302 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, AHRARNT_01, RNGTGGGC_UNKNOWN, GNF2_RTN1, ELVIDGE_HYPOXIA_DN, RRAGTTGT_UNKNOWN, AAGCAAT_MIR137, GOBP_COGNITION, GOBP_BEHAVIOR, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, TGCACTT_MIR519C_MIR519B_MIR519A, PEREZ_TP63_TARGETS, GCANCTGNY_MYOD_Q6, CMYB_01

GO Biological Process (6): sensory perception of sound (GO:0007605), locomotory behavior (GO:0007626), inner ear morphogenesis (GO:0042472), animal organ development (GO:0048513), cognition (GO:0050890), cochlea development (GO:0090102)

GO Molecular Function (3): zinc ion binding (GO:0008270), SUMO polymer binding (GO:0032184), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
inner ear development	2
anatomical structure development	2
sensory perception of mechanical stimulus	1
behavior	1
ear morphogenesis	1
embryonic morphogenesis	1
nervous system process	1
transition metal ion binding	1
SUMO binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SOBP	PACSIN1	Q9BY11	803
SOBP	RIPPLY1	Q0D2K3	409
SOBP	PTK7	Q13308	408
SOBP	SIMC1	Q8NDZ2	390
SOBP	VANGL2	Q9ULK5	367
SOBP	QRSL1	Q9H0R6	363
SOBP	SEC63	Q9UGP8	353
SOBP	PPP1R14B	Q96C90	352
SOBP	CYB5R4	Q7L1T6	352
SOBP	ARHGAP20	Q9P2F6	350
SOBP	SCML4	Q8N228	348
SOBP	MTRES1	Q9P0P8	348
SOBP	LMX1B	O60663	347
SOBP	RTN4IP1	Q8WWV3	333
SOBP	CFAP44	Q96MT7	321

IntAct

6 interactions, top by confidence:

A	B	Type	Score
CTBP1	SOBP	psi-mi:“MI:0915”(physical association)	0.550
CTBP1	GSN	psi-mi:“MI:0914”(association)	0.350
MIF	BLTP3B	psi-mi:“MI:0914”(association)	0.350
SOX6	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
CELF3	SOBP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (10): SUMO2 (Reconstituted Complex), SOBP (Affinity Capture-RNA), SOBP (Protein-peptide), SOBP (Affinity Capture-RNA), SOBP (Two-hybrid), SOBP (Proximity Label-MS), SOBP (Affinity Capture-MS), SOBP (Proximity Label-MS), SOBP (Proximity Label-MS), SOBP (Two-hybrid)

ESM2 similar proteins: A0JLT2, A3KMN5, A7XYH9, A7XYI6, A7XYQ1, B3DM43, F1M8W4, O42400, O94885, P35710, P35711, P40647, P43322, P57094, P57095, P59808, P78312, Q02297, Q05199, Q08495, Q08C81, Q08DM1, Q0P5V2, Q32NP7, Q3UH68, Q52KW0, Q569H4, Q56A10, Q5F368, Q5R4B6, Q5R8Q8, Q5U2R6, Q6DR98, Q6PD31, Q7TQG1, Q80Z38, Q8BLB8, Q8C1B1, Q8C1S0, Q8CGI1

Diamond homologs: A5X7A0, A7XYH5, A7XYH9, A7XYI6, A7XYJ6, A7XYQ1, Q0P5V2, Q9Y5P3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	147
Likely benign	36
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2149 predictions. Top by Δscore:

Variant	Effect	Δscore
6:107503655:A:AG	acceptor_gain	1.0000
6:107503656:G:GG	acceptor_gain	1.0000
6:107503656:GA:G	acceptor_gain	1.0000
6:107503656:GAAC:G	acceptor_gain	1.0000
6:107503656:GAACT:G	acceptor_gain	1.0000
6:107503792:AAAGG:A	donor_loss	1.0000
6:107503793:AAGG:A	donor_loss	1.0000
6:107503795:GGTA:G	donor_loss	1.0000
6:107503796:GTAAT:G	donor_loss	1.0000
6:107503797:T:A	donor_loss	1.0000
6:107506236:TTACA:T	acceptor_loss	1.0000
6:107506237:TACAG:T	acceptor_loss	1.0000
6:107506238:ACAGA:A	acceptor_loss	1.0000
6:107506239:CA:C	acceptor_loss	1.0000
6:107506240:A:AG	acceptor_gain	1.0000
6:107506241:G:A	acceptor_loss	1.0000
6:107506241:G:GA	acceptor_gain	1.0000
6:107506241:GAA:G	acceptor_gain	1.0000
6:107506241:GAAA:G	acceptor_gain	1.0000
6:107531063:C:G	donor_gain	1.0000
6:107531373:GAATT:G	donor_gain	1.0000
6:107533457:A:AG	acceptor_gain	1.0000
6:107533458:G:GG	acceptor_gain	1.0000
6:107533608:AAGGT:A	donor_loss	1.0000
6:107533611:G:T	donor_loss	1.0000
6:107533612:T:A	donor_loss	1.0000
6:107587176:G:GG	donor_gain	1.0000
6:107490667:G:GT	donor_gain	0.9900
6:107490691:G:GT	donor_gain	0.9900
6:107499221:A:G	donor_gain	0.9900

AlphaMissense

5717 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:107490666:G:C	R17T	1.000
6:107490666:G:T	R17M	1.000
6:107490667:G:C	R17S	1.000
6:107490667:G:T	R17S	1.000
6:107490668:A:G	K18E	1.000
6:107490670:G:C	K18N	1.000
6:107490670:G:T	K18N	1.000
6:107490675:C:A	A20D	1.000
6:107490677:C:G	H21D	1.000
6:107490679:C:A	H21Q	1.000
6:107490679:C:G	H21Q	1.000
6:107490688:A:C	K24N	1.000
6:107490688:A:T	K24N	1.000
6:107490690:G:T	R25M	1.000
6:107490691:G:C	R25S	1.000
6:107490691:G:T	R25S	1.000
6:107503685:T:A	L42H	1.000
6:107503685:T:C	L42P	1.000
6:107503685:T:G	L42R	1.000
6:107503688:T:A	L43H	1.000
6:107503688:T:C	L43P	1.000
6:107503693:T:A	W45R	1.000
6:107503693:T:C	W45R	1.000
6:107503695:G:C	W45C	1.000
6:107503695:G:T	W45C	1.000
6:107533483:T:A	I149K	1.000
6:107533483:T:G	I149R	1.000
6:107533488:T:A	C151S	1.000
6:107533488:T:C	C151R	1.000
6:107533488:T:G	C151G	1.000

dbSNP variants (sampled 300 via entrez): RS1000019237 (6:107566626 G>A), RS1000077976 (6:107569944 G>A,T), RS1000101344 (6:107604624 C>G), RS1000194879 (6:107526515 C>G,T), RS1000197169 (6:107570806 A>G), RS1000200816 (6:107650723 G>A), RS1000247676 (6:107489546 G>C), RS1000254562 (6:107622873 T>C), RS1000259441 (6:107563932 C>G,T), RS1000273078 (6:107583156 A>G), RS1000319116 (6:107557460 C>G), RS1000337774 (6:107533274 A>G), RS1000385946 (6:107609795 G>A), RS1000396827 (6:107656129 A>C,G), RS1000407344 (6:107602169 T>C)

Disease associations

OMIM: gene MIM:613667 | disease phenotypes: MIM:613671

GenCC curated gene-disease

Disease	Classification	Inheritance
intellectual disability, anterior maxillary protrusion, and strabismus	Supportive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
syndromic intellectual disability	Limited	AR

Mondo (1): intellectual disability, anterior maxillary protrusion, and strabismus (MONDO:0013353)

Orphanet (1): Anterior maxillary protrusion-strabismus-intellectual disability syndrome (Orphanet:562559)

HPO phenotypes

17 total (17 of 17 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000486	Strabismus
HP:0000505	Visual impairment
HP:0000540	Hypermetropia
HP:0000565	Esotropia
HP:0000646	Amblyopia
HP:0000678	Dental crowding
HP:0000709	Psychosis
HP:0000736	Short attention span
HP:0000750	Delayed speech and language development
HP:0001263	Global developmental delay
HP:0001382	Joint hypermobility
HP:0002465	Poor speech
HP:0003593	Infantile onset
HP:0010807	Open bite
HP:0010864	Severe intellectual disability
HP:0430028	Hyperplasia of the maxilla

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006979_377	Heel bone mineral density	3.000000e-16
GCST008839_571	Height	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, decreases expression, increases expression	4
methylmercuric chloride	decreases expression, increases expression	3
Estradiol	increases expression, increases reaction, affects cotreatment	3
trichostatin A	decreases expression, increases expression, affects cotreatment	2
mercuric bromide	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
bisphenol A	increases expression	1
testosterone undecanoate	affects cotreatment, increases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
NSC 689534	decreases expression, affects binding	1
NSC668394	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Caffeine	decreases phosphorylation	1

Clinical trials (associated diseases)

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