SALL2

Summary

SALL2 (spalt like transcription factor 2, HGNC:10526) is a protein-coding gene on chromosome 14q11.2, encoding Sal-like protein 2 (Q9Y467). Probable transcription factor that plays a role in eye development before, during, and after optic fissure closure.

This gene encodes a protein containing multiple zinc finger domains. The encoded protein functions in optical fissure closure during development of the eye in the embryo. Mutations in this gene are associated with ocular coloboma.

Source: NCBI Gene 6297 — RefSeq curated summary.

At a glance

• Gene–disease (curated): coloboma, ocular, autosomal recessive (Limited, GenCC)
• GWAS associations: 4
• Clinical variants (ClinVar): 214 total — 1 pathogenic
• Phenotypes (HPO): 11
• MANE Select transcript: NM_001364564

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10526
Approved symbol	SALL2
Name	spalt like transcription factor 2
Location	14q11.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0360, Hsal2, ZNF795
Ensembl gene	ENSG00000165821
Ensembl biotype	protein_coding
OMIM	602219
Entrez	6297

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000450879, ENST00000537235, ENST00000541965, ENST00000546363, ENST00000611430, ENST00000613414, ENST00000614342

RefSeq mRNA: 4 — MANE Select: NM_001364564 NM_001291446, NM_001291447, NM_001364564, NM_005407

CCDS: CCDS32045, CCDS76656, CCDS91849

Canonical transcript exons

ENST00000537235 — 2 exons

Exon	Start	End
ENSE00002207780	21521080	21525654
ENSE00002305533	21526061	21526346

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 96.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.4682 / max 452.2007, expressed in 1314 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
142192	6.1483	1070
142193	4.3695	1128
142198	2.1186	235
142199	0.4613	182
142196	0.4065	163
142197	0.2781	148
142194	0.2458	101
142191	0.1874	84
142183	0.1748	91
142195	0.0779	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	96.23	gold quality
superior vestibular nucleus	UBERON:0007227	95.71	gold quality
paraflocculus	UBERON:0005351	95.68	gold quality
ventral tegmental area	UBERON:0002691	95.54	gold quality
ventricular zone	UBERON:0003053	95.29	gold quality
medulla oblongata	UBERON:0001896	94.88	gold quality
inferior olivary complex	UBERON:0002127	94.86	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.84	gold quality
cerebellar cortex	UBERON:0002129	94.80	gold quality
cerebellum	UBERON:0002037	94.78	gold quality
cerebellar hemisphere	UBERON:0002245	94.77	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	94.35	gold quality
pons	UBERON:0000988	93.77	gold quality
oocyte	CL:0000023	93.45	gold quality
hypothalamus	UBERON:0001898	93.11	gold quality
embryo	UBERON:0000922	92.83	gold quality
cranial nerve II	UBERON:0000941	92.77	gold quality
dorsal plus ventral thalamus	UBERON:0001897	92.52	gold quality
subthalamic nucleus	UBERON:0001906	92.25	gold quality
inferior vagus X ganglion	UBERON:0005363	91.78	gold quality
midbrain	UBERON:0001891	91.48	gold quality
caudate nucleus	UBERON:0001873	91.36	gold quality
nucleus accumbens	UBERON:0001882	91.31	gold quality
putamen	UBERON:0001874	91.21	gold quality
substantia nigra	UBERON:0002038	91.12	gold quality
ganglionic eminence	UBERON:0004023	90.95	gold quality
CA1 field of hippocampus	UBERON:0003881	90.93	gold quality
entorhinal cortex	UBERON:0002728	90.77	gold quality
substantia nigra pars compacta	UBERON:0001965	90.61	gold quality
lateral globus pallidus	UBERON:0002476	90.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-9388	yes	11.27
E-ANND-3	yes	3.35

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

7 targets.

Target	Regulation
ABL1
BAX
CDKN1A	Unknown
LARGE1
SALL2
TBXT
TP53	Activation

Upstream regulators (CollecTRI, top): SALL2, TFAP4, TGFB1, TP53, WT1

miRNA regulators (miRDB)

74 targeting SALL2, 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-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084

Literature-anchored findings (GeneRIF, showing 16)

• Epidermal growth factor receptor (a potential therapeutic target) and SALL2 stained most cases of synovial sarcoma; staining was significantly less common among other tested sarcomas. (PMID:14507652)
• Results suggest that p150(Sal2), acting in part as a p53-independent regulator of p21 and BAX, can function in some cell types as a regulator of cell growth and survival [p150(Sal2)] (PMID:15082782)
• These data establish Sall2 as a link between p75 neurotrophin receptor and transcriptional events that regulate the growth and development of neuronal cells. (PMID:19131967)
• Studies indicate that vertebrate sal orthologues (spalt-like/sall) have important developmental roles during neural development and organogenesis and gentic diseases. (PMID:19247946)
• A CUL4/DDB1 E3 ligase containing RBBP7 as the p150(Sal2) receptor has been identified as mediating the destruction of p150(Sal2) as cells transition from a quiescent to an actively growing state. (PMID:21228219)
• Results demonstrate binding of p150(Sal2) to two natural promoters with GC elements related to the optimal binding sequence defined in vitro and whose regulation is important for suppression of tumor growth. (PMID:21362508)
• Here, the authors report that human papillomavirus type 16 E6 targets the cellular factor p150(Sal2), which positively regulates p21(WAF1) transcription. (PMID:21791360)
• c-MYC may come under negative regulation by p150, consistent with the action of p150 as a putative tumor suppressor. (PMID:23029531)
• The SALL2 P2 promoter is hypermethylated in a majority of serous ovarian carcinomas. (PMID:23273547)
• A role for SALL2 in eye morphogenesis and loss of function of the gene causes ocular coloboma in humans and mice. (PMID:24412933)
• Sall2 enhanced the p16 minigene blocking of cell cycle progression and p16 knockdown with siRNA abolished most of the Sall2 inhibition of cell cycle progression (PMID:25580951)
• Mechanisms of silencing SALL2 in OVCA cell lines and primary tumors and possible therapeutic approaches for ovarian carcinoma are discussed in this review. (PMID:25608837)
• Understanding SALL2 function and the molecular mechanisms governing its expression and activity is critical to comprehend why and how SALL2 could contribute to disease. This knowledge will open new perspectives for the development of molecular targeted approaches in disease (PMID:28430874)
• Using RNA interference, the role of Spalt-like gene-2 (SALL2) was investigated in human ovarian carcinoma (OC) A2780 cells. Found downregulation of SALL2 promoted growth of the OC cell line. (PMID:29228922)
• Sall2 may play a significant role in NIT-1 cell function. (PMID:29783189)
• SALL2 methylation statistically correlated with a decrease in disease free survival in patients with oral squamous carcinoma. (PMID:31188017)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	Sall2	ENSMUSG00000049532
rattus_norvegicus	Sall2	ENSRNOG00000013287
drosophila_melanogaster	salr	FBGN0000287
drosophila_melanogaster	Cph	FBGN0029939
drosophila_melanogaster	salm	FBGN0261648
caenorhabditis_elegans	sem-4	WBGENE00004773
caenorhabditis_elegans		WBGENE00017430

Paralogs (14): HIVEP2 (ENSG00000010818), HIVEP1 (ENSG00000095951), SALL4 (ENSG00000101115), ZNF516 (ENSG00000101493), SALL1 (ENSG00000103449), BCL11A (ENSG00000119866), ZNF831 (ENSG00000124203), RREB1 (ENSG00000124782), HIVEP3 (ENSG00000127124), BCL11B (ENSG00000127152), ZNF219 (ENSG00000165804), ZNF217 (ENSG00000171940), ZNF536 (ENSG00000198597), SALL3 (ENSG00000256463)

Protein

Protein identifiers

Sal-like protein 2 — Q9Y467 (reviewed: Q9Y467)

Alternative names: Zinc finger protein 795, Zinc finger protein SALL2, Zinc finger protein Spalt-2

All UniProt accessions (7): A0A087X1T9, A0A0B4J2F7, E7EW59, Q9Y467, F5H1G6, F5H433, H0YFS7

UniProt curated annotations — full annotation on UniProt →

Function. Probable transcription factor that plays a role in eye development before, during, and after optic fissure closure.

Subcellular location. Nucleus.

Tissue specificity. Highest levels in adult brain (in different areas). Lower levels in heart; very low levels in kidney and pancreas. Expressed throughout the retina and lens vesicle as well as the periocular mesenchyme.

Disease relevance. Coloboma, ocular, autosomal recessive (COAR) [MIM:216820] An ocular anomaly resulting from abnormal morphogenesis of the optic cup and stalk, and incomplete fusion of the fetal intra-ocular fissure during gestation. The clinical presentation is variable. Some individuals may present with minimal defects in the anterior iris leaf without other ocular defects. More complex malformations create a combination of iris, uveoretinal and/or optic nerve defects without or with microphthalmia or even anophthalmia. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the sal C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y467-1	1	yes
Q9Y467-3	2

RefSeq proteins (4): NP_001278375, NP_001278376, NP_001351493, NP_005398 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR051565	Sal_C2H2-zinc-finger	Family

Pfam: PF00096, PF13912

UniProt features (39 total): zinc finger region 8, region of interest 8, compositionally biased region 8, modified residue 4, splice variant 3, sequence variant 3, sequence conflict 3, chain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y467-F1	52.09	0.03

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 (5): 243, 797, 802, 806, 911

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, LI_WILMS_TUMOR, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, MODULE_118, BLALOCK_ALZHEIMERS_DISEASE_UP, GATA6_01, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN, DELYS_THYROID_CANCER_DN, GRE_C, CYTAGCAAY_UNKNOWN, TCCAGAG_MIR518C, GOBP_SENSORY_ORGAN_DEVELOPMENT, CONRAD_STEM_CELL, MODULE_397, KAYO_AGING_MUSCLE_UP

GO Biological Process (4): eye development (GO:0001654), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944), system development (GO:0048731)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), 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
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
sensory organ development	1
visual system development	1
regulation of DNA-templated transcription	1
positive regulation of DNA-templated transcription	1
multicellular organism development	1
anatomical structure development	1
transcription cis-regulatory region binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1054 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SALL2	POU3F2	P20265	827
SALL2	OLIG2	Q13516	609
SALL2	SOX2	P48431	579
SALL2	SHOX2	O60902	534
SALL2	STRA6	Q9BX79	505
SALL2	ABCB6	Q9NP58	438
SALL2	SIX1	Q15475	434
SALL2	GDF6	Q6KF10	433
SALL2	METTL3	Q86U44	433
SALL2	ABHD4	Q8TB40	418
SALL2	DAD1	P46966	416
SALL2	TOX4	O94842	415
SALL2	POU5F1	P31359	400
SALL2	KLF17	Q5JT82	381
SALL2	TENM3	Q9P273	379

IntAct

88 interactions, top by confidence:

A	B	Type	Score
CEP76	SALL2	psi-mi:“MI:0915”(physical association)	0.670
ZC3HC1	TPR	psi-mi:“MI:0914”(association)	0.640
SALL2	NGFR	psi-mi:“MI:0915”(physical association)	0.580
NGFR	SALL2	psi-mi:“MI:0915”(physical association)	0.580
ZMIZ2	SALL2	psi-mi:“MI:0915”(physical association)	0.560
SALL2	ZMIZ2	psi-mi:“MI:0915”(physical association)	0.560
ASB7	POLR3A	psi-mi:“MI:0914”(association)	0.530
DSN1	EXOC5	psi-mi:“MI:0914”(association)	0.530
SALL2	GFPT2	psi-mi:“MI:0914”(association)	0.530
SALL1	TIMM50	psi-mi:“MI:0914”(association)	0.530
SV2A	EXTL3	psi-mi:“MI:0914”(association)	0.530
SALL2	ADAMTSL4	psi-mi:“MI:0915”(physical association)	0.490
SOX2	SALL2	psi-mi:“MI:0915”(physical association)	0.400
SALL2	rep	psi-mi:“MI:0915”(physical association)	0.370
SALL2	ZMIZ2	psi-mi:“MI:0915”(physical association)	0.370
EWSR1	SALL2	psi-mi:“MI:0915”(physical association)	0.370
IRF3	FASN	psi-mi:“MI:0914”(association)	0.350
PRMT2	KRBA1	psi-mi:“MI:0914”(association)	0.350
CDC16	KRBA1	psi-mi:“MI:0914”(association)	0.350
RFPL4B	KRBA1	psi-mi:“MI:0914”(association)	0.350
ASB3	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
PSME3	ZNF891	psi-mi:“MI:0914”(association)	0.350

BioGRID (135): CEP76 (Two-hybrid), ZMIZ2 (Two-hybrid), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS), CEP76 (Two-hybrid), ZMIZ2 (Two-hybrid), SALL2 (Two-hybrid), SALL2 (Affinity Capture-MS), SALL2 (Affinity Capture-MS)

ESM2 similar proteins: A2A5E6, A5PK23, A6NKF2, A6PWV5, B0K011, E9Q6W4, O02786, O95402, P09086, P13297, P55198, Q00196, Q08DS3, Q0VDQ9, Q29013, Q2NKI2, Q2VL80, Q2VL82, Q2VL83, Q2VL85, Q2VL86, Q569K4, Q5XI28, Q62255, Q66K41, Q6AXX3, Q6PBT9, Q86V15, Q8BXJ8, Q8IVH2, Q8K4J6, Q8TAX0, Q8VD12, Q8VDL9, Q8WUU4, Q92766, Q969V6, Q96PM9, Q9BXA9, Q9BZE0

Diamond homologs: B0K011, B0X9H6, E9Q6W4, O75362, O77459, P28698, P31509, P60319, P80944, P86413, Q01798, Q02026, Q02027, Q08DS3, Q0IHB8, Q292R5, Q29419, Q32NK7, Q3T135, Q3US17, Q567J8, Q5SVQ8, Q5XJQ7, Q66JF8, Q6AY34, Q6ZNH5, Q811F1, Q8BX22, Q8BY46, Q8N2R0, Q8TAX0, Q8TBZ5, Q8WUU4, Q91ZD1, Q99PV8, Q9C0K0, Q9H165, Q9H4T2, Q9QX96, Q9QYE3

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
TFAP4	“up-regulates quantity by expression”	SALL2	“transcriptional regulation”
TGFB1	“down-regulates quantity by repression”	SALL2	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 105 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
mRNA Splicing	6	9.6×	3e-03
mRNA Polyadenylation	7	8.9×	2e-03
Processing of Capped Intron-Containing Pre-mRNA	7	8.3×	2e-03
mRNA Splicing - Major Pathway	9	7.1×	8e-04
Dengue Virus-Host Interactions	10	6.6×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	157
Likely benign	34
Benign	18

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
143946	NM_001364564.1(SALL2):c.79G>T (p.Glu27Ter)	Pathogenic

SpliceAI

471 predictions. Top by Δscore:

Variant	Effect	Δscore
14:21526629:AG:A	donor_gain	1.0000
14:21526629:AGC:A	donor_gain	1.0000
14:21526629:AGCC:A	donor_gain	1.0000
14:21529355:C:A	donor_gain	1.0000
14:21526630:G:C	donor_gain	0.9900
14:21526631:C:CA	donor_gain	0.9900
14:21526666:A:AC	donor_gain	0.9900
14:21536847:A:AT	donor_loss	0.9900
14:21536848:CCGTT:C	donor_gain	0.9900
14:21526639:A:AC	donor_gain	0.9800
14:21526660:T:TA	donor_gain	0.9800
14:21525654:CCTG:C	acceptor_loss	0.9700
14:21525656:T:C	acceptor_loss	0.9700
14:21529354:T:TA	donor_gain	0.9700
14:21536847:A:AC	donor_gain	0.9700
14:21536848:C:CC	donor_gain	0.9700
14:21526629:A:AC	donor_gain	0.9600
14:21526667:T:C	donor_gain	0.9600
14:21525534:A:AC	donor_gain	0.9500
14:21536888:A:C	donor_gain	0.9400
14:21526062:T:TA	donor_gain	0.9300
14:21525655:C:CC	acceptor_gain	0.9200
14:21526595:C:A	donor_gain	0.9200
14:21526640:G:C	donor_gain	0.9200
14:21536847:AC:A	donor_gain	0.9200
14:21536848:CC:C	donor_gain	0.9200
14:21536863:CTGGG:C	donor_gain	0.9200
14:21536867:G:T	donor_gain	0.9100
14:21526751:C:CT	acceptor_gain	0.9000
14:21536864:TGGG:T	donor_gain	0.9000

AlphaMissense

6476 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:21523628:G:C	F700L	1.000
14:21523628:G:T	F700L	1.000
14:21523629:A:G	F700S	1.000
14:21523630:A:G	F700L	1.000
14:21523640:G:C	C696W	1.000
14:21523641:C:T	C696Y	1.000
14:21523642:A:G	C696R	1.000
14:21523649:G:C	C693W	1.000
14:21523651:A:G	C693R	1.000
14:21523707:A:G	L674P	1.000
14:21523724:G:C	F668L	1.000
14:21523724:G:T	F668L	1.000
14:21523725:A:C	F668C	1.000
14:21523725:A:G	F668S	1.000
14:21523726:A:G	F668L	1.000
14:21523737:C:T	C664Y	1.000
14:21523738:A:G	C664R	1.000
14:21523745:G:C	C661W	1.000
14:21523746:C:G	C661S	1.000
14:21523746:C:T	C661Y	1.000
14:21523747:A:G	C661R	1.000
14:21523747:A:T	C661S	1.000
14:21523751:G:C	F659L	1.000
14:21523751:G:T	F659L	1.000
14:21523753:A:G	F659L	1.000
14:21523783:G:C	H649D	1.000
14:21523791:A:G	L646P	1.000
14:21523820:A:C	C636W	1.000
14:21523821:C:T	C636Y	1.000
14:21523822:A:G	C636R	1.000

dbSNP variants (sampled 300 via entrez): RS1000192551 (14:21522316 C>G), RS1000238765 (14:21534851 C>T), RS1000251001 (14:21529153 G>C), RS1000303361 (14:21528739 C>G), RS1000411952 (14:21526215 C>G), RS1000453938 (14:21535039 A>G,T), RS1000579393 (14:21523251 T>A), RS1000583501 (14:21530814 T>C), RS1001015550 (14:21527800 C>A,G,T), RS1001081323 (14:21520757 AAC>A), RS1001443687 (14:21528133 C>T), RS1001780918 (14:21533052 C>T), RS1001855 (14:21530782 A>G), RS1002198668 (14:21525211 C>T), RS1002249937 (14:21537248 T>A,C)

Disease associations

OMIM: gene MIM:602219 | disease phenotypes: MIM:216820

GenCC curated gene-disease

Disease	Classification	Inheritance
coloboma, ocular, autosomal recessive	Limited	Unknown

Mondo (1): coloboma, ocular, autosomal recessive (MONDO:0009002)

Orphanet (1): OBSOLETE: Ocular coloboma (Orphanet:194)

HPO phenotypes

11 total (11 of 11 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000480	Retinal coloboma
HP:0000518	Cataract
HP:0000565	Esotropia
HP:0000577	Exotropia
HP:0000588	Optic disc coloboma
HP:0000612	Iris coloboma
HP:0000639	Nystagmus
HP:0001132	Lens subluxation
HP:0007663	Reduced visual acuity
HP:0025586	Hypertropia

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002749_4	Response to Homoharringtonine (cytotoxicity)	9.000000e-07
GCST007231_8	Tuberculosis	6.000000e-06
GCST010136_27	Fruit consumption	5.000000e-19
GCST012490_46	Femur bone mineral density x serum urate levels interaction	1.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006952	cytotoxicity measurement
EFO:0008111	diet measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	8
bisphenol A	increases methylation, affects cotreatment, decreases expression, increases expression	5
trichostatin A	affects cotreatment, decreases expression	3
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cyclosporine	decreases expression	2
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases abundance, decreases expression	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Zoledronic Acid	decreases expression	1
Vorinostat	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	increases expression	1
Doxorubicin	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XV80	HEK293 eGFP-SALL2	Transformed cell line	Female

Clinical trials (associated diseases)

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