Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Entrez ID	6297
Gene name	Spalt like transcription factor 2
Gene symbol	SALL2
Synonyms (NCBI Gene)	COLBHSAL2Sal-2ZNF795p150(Sal2)
Chromosome	14
Chromosome location	14q11.2
Summary	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. [provided by RefSeq, Jul

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SNP ID	Visualize variation	Clinical significance	Consequence
rs587776429	C>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant

150

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miRTarBase ID	miRNA	Experiments	Reference
MIRT052046	hsa-let-7b-5p	CLASH	23622248
MIRT048695	hsa-miR-99a-5p	CLASH	23622248
MIRT043322	hsa-miR-331-3p	CLASH	23622248
MIRT042308	hsa-miR-484	CLASH	23622248
MIRT039723	hsa-miR-615-3p	CLASH	23622248
MIRT038599	hsa-miR-106b-3p	CLASH	23622248
MIRT458335	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT458336	hsa-miR-6798-5p	PAR-CLIP	23592263
MIRT458334	hsa-miR-3185	PAR-CLIP	23592263
MIRT458333	hsa-miR-1252-5p	PAR-CLIP	23592263
MIRT458332	hsa-miR-1909-3p	PAR-CLIP	23592263
MIRT458331	hsa-miR-6722-3p	PAR-CLIP	23592263
MIRT458330	hsa-miR-1-3p	PAR-CLIP	23592263
MIRT458329	hsa-miR-206	PAR-CLIP	23592263
MIRT458328	hsa-miR-613	PAR-CLIP	23592263
MIRT458327	hsa-miR-6081	PAR-CLIP	23592263
MIRT458326	hsa-miR-766-5p	PAR-CLIP	23592263
MIRT458325	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT458324	hsa-miR-6825-5p	PAR-CLIP	23592263
MIRT458323	hsa-miR-4723-5p	PAR-CLIP	23592263
MIRT458322	hsa-miR-5698	PAR-CLIP	23592263
MIRT458321	hsa-miR-6870-5p	PAR-CLIP	23592263
MIRT458320	hsa-miR-7111-5p	PAR-CLIP	23592263
MIRT458335	hsa-miR-6510-5p	PAR-CLIP	23592263
MIRT458336	hsa-miR-6798-5p	PAR-CLIP	23592263
MIRT458334	hsa-miR-3185	PAR-CLIP	23592263
MIRT458333	hsa-miR-1252-5p	PAR-CLIP	23592263
MIRT458332	hsa-miR-1909-3p	PAR-CLIP	23592263
MIRT458331	hsa-miR-6722-3p	PAR-CLIP	23592263
MIRT458330	hsa-miR-1-3p	PAR-CLIP	23592263
MIRT458329	hsa-miR-206	PAR-CLIP	23592263
MIRT458328	hsa-miR-613	PAR-CLIP	23592263
MIRT458327	hsa-miR-6081	PAR-CLIP	23592263
MIRT458326	hsa-miR-766-5p	PAR-CLIP	23592263
MIRT458325	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT458324	hsa-miR-6825-5p	PAR-CLIP	23592263
MIRT458323	hsa-miR-4723-5p	PAR-CLIP	23592263
MIRT458322	hsa-miR-5698	PAR-CLIP	23592263
MIRT458321	hsa-miR-6870-5p	PAR-CLIP	23592263
MIRT458320	hsa-miR-7111-5p	PAR-CLIP	23592263
MIRT1324908	hsa-miR-1237	CLIP-seq
MIRT1324909	hsa-miR-1299	CLIP-seq
MIRT1324910	hsa-miR-185	CLIP-seq
MIRT1324911	hsa-miR-1909	CLIP-seq
MIRT1324912	hsa-miR-3150b-3p	CLIP-seq
MIRT1324913	hsa-miR-361-3p	CLIP-seq
MIRT1324914	hsa-miR-4271	CLIP-seq
MIRT1324915	hsa-miR-4306	CLIP-seq
MIRT1324916	hsa-miR-4496	CLIP-seq
MIRT1324917	hsa-miR-4644	CLIP-seq
MIRT1324918	hsa-miR-4716-3p	CLIP-seq
MIRT1324919	hsa-miR-4725-3p	CLIP-seq
MIRT1324920	hsa-miR-4779	CLIP-seq
MIRT1324921	hsa-miR-4782-5p	CLIP-seq
MIRT1324922	hsa-miR-4784	CLIP-seq
MIRT1324923	hsa-miR-516b	CLIP-seq
MIRT1324924	hsa-miR-605	CLIP-seq
MIRT1324925	hsa-miR-625	CLIP-seq
MIRT1324908	hsa-miR-1237	CLIP-seq
MIRT2096452	hsa-miR-1245b-5p	CLIP-seq
MIRT1324909	hsa-miR-1299	CLIP-seq
MIRT2096453	hsa-miR-1304	CLIP-seq
MIRT1324910	hsa-miR-185	CLIP-seq
MIRT1324911	hsa-miR-1909	CLIP-seq
MIRT2096454	hsa-miR-204	CLIP-seq
MIRT2096455	hsa-miR-211	CLIP-seq
MIRT2096456	hsa-miR-3142	CLIP-seq
MIRT1324912	hsa-miR-3150b-3p	CLIP-seq
MIRT2096457	hsa-miR-3153	CLIP-seq
MIRT2096458	hsa-miR-4270	CLIP-seq
MIRT1324914	hsa-miR-4271	CLIP-seq
MIRT2096459	hsa-miR-4292	CLIP-seq
MIRT1324915	hsa-miR-4306	CLIP-seq
MIRT2096460	hsa-miR-4308	CLIP-seq
MIRT2096461	hsa-miR-4441	CLIP-seq
MIRT2096462	hsa-miR-4446-5p	CLIP-seq
MIRT1324917	hsa-miR-4644	CLIP-seq
MIRT1324918	hsa-miR-4716-3p	CLIP-seq
MIRT1324919	hsa-miR-4725-3p	CLIP-seq
MIRT2096463	hsa-miR-4755-5p	CLIP-seq
MIRT1324920	hsa-miR-4779	CLIP-seq
MIRT1324921	hsa-miR-4782-5p	CLIP-seq
MIRT1324922	hsa-miR-4784	CLIP-seq
MIRT2096464	hsa-miR-499-3p	CLIP-seq
MIRT2096465	hsa-miR-499a-3p	CLIP-seq
MIRT1324923	hsa-miR-516b	CLIP-seq
MIRT2096466	hsa-miR-618	CLIP-seq
MIRT2096467	hsa-miR-623	CLIP-seq
MIRT1324925	hsa-miR-625	CLIP-seq
MIRT2320637	hsa-miR-1207-5p	CLIP-seq
MIRT2320638	hsa-miR-1321	CLIP-seq
MIRT2320639	hsa-miR-1827	CLIP-seq
MIRT2096458	hsa-miR-4270	CLIP-seq
MIRT2096461	hsa-miR-4441	CLIP-seq
MIRT2320640	hsa-miR-4739	CLIP-seq
MIRT2320641	hsa-miR-4756-5p	CLIP-seq
MIRT2320642	hsa-miR-4763-3p	CLIP-seq
MIRT2320643	hsa-miR-940	CLIP-seq
MIRT2616656	hsa-miR-1276	CLIP-seq
MIRT2616657	hsa-miR-15a	CLIP-seq
MIRT2616658	hsa-miR-15b	CLIP-seq
MIRT2616659	hsa-miR-16	CLIP-seq
MIRT2616660	hsa-miR-181a	CLIP-seq
MIRT2616661	hsa-miR-181b	CLIP-seq
MIRT2616662	hsa-miR-181c	CLIP-seq
MIRT2616663	hsa-miR-181d	CLIP-seq
MIRT2616664	hsa-miR-186	CLIP-seq
MIRT2616665	hsa-miR-195	CLIP-seq
MIRT2616666	hsa-miR-214	CLIP-seq
MIRT2616667	hsa-miR-2278	CLIP-seq
MIRT2616668	hsa-miR-3619-5p	CLIP-seq
MIRT2616669	hsa-miR-424	CLIP-seq
MIRT2616670	hsa-miR-4262	CLIP-seq
MIRT2616671	hsa-miR-4457	CLIP-seq
MIRT2616672	hsa-miR-497	CLIP-seq
MIRT2616673	hsa-miR-513b	CLIP-seq
MIRT1324923	hsa-miR-516b	CLIP-seq
MIRT2616674	hsa-miR-668	CLIP-seq
MIRT2616675	hsa-miR-761	CLIP-seq
MIRT2690165	hsa-miR-1202	CLIP-seq
MIRT2690166	hsa-miR-1224-5p	CLIP-seq
MIRT2690167	hsa-miR-1258	CLIP-seq
MIRT2616656	hsa-miR-1276	CLIP-seq
MIRT2690168	hsa-miR-129-3p	CLIP-seq
MIRT2690169	hsa-miR-154	CLIP-seq
MIRT2616657	hsa-miR-15a	CLIP-seq
MIRT2616658	hsa-miR-15b	CLIP-seq
MIRT2616659	hsa-miR-16	CLIP-seq
MIRT2616665	hsa-miR-195	CLIP-seq
MIRT2616666	hsa-miR-214	CLIP-seq
MIRT2690170	hsa-miR-22	CLIP-seq
MIRT2616667	hsa-miR-2278	CLIP-seq
MIRT2690171	hsa-miR-296-5p	CLIP-seq
MIRT1324912	hsa-miR-3150b-3p	CLIP-seq
MIRT2690172	hsa-miR-3194-5p	CLIP-seq
MIRT2616668	hsa-miR-3619-5p	CLIP-seq
MIRT2690173	hsa-miR-3915	CLIP-seq
MIRT2690174	hsa-miR-3972	CLIP-seq
MIRT2616669	hsa-miR-424	CLIP-seq
MIRT2690175	hsa-miR-4290	CLIP-seq
MIRT2690176	hsa-miR-4434	CLIP-seq
MIRT2690177	hsa-miR-4476	CLIP-seq
MIRT2690178	hsa-miR-4516	CLIP-seq
MIRT2690179	hsa-miR-4689	CLIP-seq
MIRT1324922	hsa-miR-4784	CLIP-seq
MIRT2616672	hsa-miR-497	CLIP-seq
MIRT1324923	hsa-miR-516b	CLIP-seq
MIRT2690180	hsa-miR-520a-5p	CLIP-seq
MIRT2690181	hsa-miR-525-5p	CLIP-seq
MIRT2616675	hsa-miR-761	CLIP-seq

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Transcription factor	Regulation	Reference
TFAP4	Activation	21228219

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA	21362508
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	21362508
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IMP	21362508
GO:0001654	Process	Eye development	IDA	24412933
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 19131967, 25416956
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	21362508
GO:0046872	Function	Metal ion binding	IEA
GO:0048731	Process	System development	IEA

MIM	HGNC	e!Ensembl
602219	10526	ENSG00000165821

Q9Y467

Protein name

Sal-like protein 2 (Zinc finger protein 795) (Zinc finger protein SALL2) (Zinc finger protein Spalt-2) (Sal-2) (hSal2)

Protein function

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

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00096	zf-C2H2	401 → 423	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	659 → 681	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	692 → 713	Zinc finger, C2H2 type	Domain
PF13912	zf-C2H2_6	912 → 936		Domain

Tissue specificity

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. {ECO:0000269|PubMed:24412933}.

Sequence

MSRRKQRKPQQLISDCEGPSASENGDASEEDHPQVCAKCCAQFTDPTEFLAHQNACSTDP
PVMVIIGGQENPNNSSASSEPRPEGHNNPQVMDTEHSNPPDSGSSVPTDPTWGPERRGEE
SPGHFLVAATGTAAGGGGGLILASPKLGATPLPPESTPAPPPPPPPPPPPGVGSGHLNIP
LILEELRVLQQRQIHQMQMTEQICRQVLLLGSLGQTVGAPASPSELPGTGTASSTKPLLP
LFSPIKPVQTSKTLASSSSSSSSSSGAETPKQAFFHLYHPLGSQHPFSAGGVGRSHKPTP
APSPALPGSTDQLIASPHLAFPSTTGLLAAQCLGAARGLEATASPGLLKPKNGSGELSYG
EVMGPLEKPGGRHKCRFCAKVFGSDSALQIHLRSHTGERPYKCNVCGNRFTTRGNLKVHF
HRHREKYPHVQMNPHPVPEHLDYVITSSGLPYGMSVPPEKAEEEAATPGGGVERKPLVAS
TTALSATESLTLLSTSAGTATAPGLPAFNKFVLMKAVEPKNKADENTPPGSEGSAISGVA
ESSTATRMQLSKLVTSLPSWALLTNHFKSTGSFPFPYVLEPLGASPSETSKLQQLVEKID
RQGAVAVTSAASGAPTTSAPAPSSSASSGPNQCVICLRVLSCPRALRLHYGQHGGERPFK
CKVCGRAFSTRGNLRAHFVGHKASPAARAQNSCPICQKKFTNAVTLQQHVRMHLGGQIPN
GGTALPEGGGAAQENGSEQSTVSGAGSFPQQQSQQPSPEEELSEEEEEEDEEEEEDVTDE
DSLAGRGSESGGEKAISVRGDSEEASGAEEEVGTVAAAATAGKEMDSNEKTTQQSSLPPP
PPPDSLDQPQPMEQGSSGVLGGKEEGGKPERSSSPASALTPEGEATSVTLVEELSLQEAM
RKEPGESSSRKACEVCGQAFPSQAALEEHQKTHPKEGPLFTCVFCRQGFLERATLKKHML
LAHHQVQPFAPHGPQNIAALSLVPGCSPSITSTGLSPFPRKDDPTIP

Sequence length

1007

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Coloboma, ocular, autosomal recessive	Pathogenic	rs587776429	RCV000133468	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (8)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CLEFT EYELID	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOBOMA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOBOMA OF CHOROID AND RETINA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOBOMA OF LENS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOBOMA OF OPTIC DISC	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL COLOBOMA OF IRIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL OCULAR COLOBOMA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SALL2-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (41)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Breast Carcinoma	Breast Carcinoma	BEFREE	31657150		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	28187708, 31657150	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	25580951	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	29228922	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	23273547, 25608837, 29228922, 29689621		★★★★★ ★☆☆☆☆ Found in Text Mining only
Coloboma of choroid and retina	Coloboma Of Eye	ORPHANET_DG	24412933		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Coloboma of lens	Lens coloboma	ORPHANET_DG	24412933		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Coloboma of optic disc	Coloboma of optic disc	ORPHANET_DG	24412933		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOBOMA, OCULAR, AUTOSOMAL RECESSIVE	Coloboma	GENOMICS_ENGLAND_DG	24412933		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
COLOBOMA, OCULAR, AUTOSOMAL RECESSIVE	Coloboma	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital coloboma of iris	Congenital Coloboma Of Iris	ORPHANET_DG	24412933		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	BEFREE	24412933, 28430874		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	28367244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	28367244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	24726434		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	24726434, 26020805, 29773872, 30497369, 34282187	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	24726434		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary macular coloboma	Coloboma of macula	ORPHANET_DG	24412933		★★★★★ ★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	BEFREE	23273547		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	31657150		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	28367244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	23273547, 25608837, 29228922, 29689621		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23029531, 28367244, 28430874, 29689621, 29778644		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	11577094, 16957934, 25608837, 29689621, 29778644		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephroblastoma	Nephroblastoma	BEFREE	11577094		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural Tube Defect	BEFREE	28430874		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Carcinoma	Ovarian Carcinoma	BEFREE	23273547, 25608837, 29228922		★★★★★ ★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	29689621		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	23273547, 29228922	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor T-cell acute lymphoblastic leukemia	Lymphoblastic Leukemia	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	Lymphoblastic Leukemia	ORPHANET_DG	29279377		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	LHGDN	14507652		★★★★★ ★☆☆☆☆ Found in Text Mining only
Sleep Deprivation	Sleep deprivation	Pubtator	17559306	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	28367244		★★★★★ ★☆☆☆☆ Found in Text Mining only
synovial sarcoma	Synovial sarcoma	LHGDN	14507652		★★★★★ ★☆☆☆☆ Found in Text Mining only
synovial sarcoma	Synovial sarcoma	BEFREE	28430874		★★★★★ ★☆☆☆☆ Found in Text Mining only
Uveoretinal Coloboma	Uveoretinal Coloboma	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Wilms Tumor	Wilms tumor	Pubtator	11577094	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

SALL2 (spalt like transcription factor 2)