SKIDA1

Summary

SKIDA1 (SKI/DACH domain containing 1, HGNC:32697) is a protein-coding gene on chromosome 10p12.31, encoding SKI/DACH domain-containing protein 1 (Q1XH10).

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of transcription by RNA polymerase II.

Source: NCBI Gene 387640 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 164 total
• MANE Select transcript: NM_207371

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32697
Approved symbol	SKIDA1
Name	SKI/DACH domain containing 1
Location	10p12.31
Locus type	gene with protein product
Status	Approved
Aliases	FLJ45187
Ensembl gene	ENSG00000180592
Ensembl biotype	protein_coding
Entrez	387640

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000444772, ENST00000449193, ENST00000487107, ENST00000633225

RefSeq mRNA: 1 — MANE Select: NM_207371 NM_207371

CCDS: CCDS44363

Canonical transcript exons

ENST00000449193 — 4 exons

Exon	Start	End
ENSE00001540292	21521389	21521480
ENSE00001540294	21523683	21523871
ENSE00001540296	21525547	21525682
ENSE00001621699	21513475	21519658

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 80.82.

FANTOM5 (CAGE): breadth broad, TPM avg 5.5235 / max 653.9018, expressed in 465 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
108623	5.2548	400
108620	0.1820	96
108622	0.0446	19
205783	0.0323	9
108617	0.0098	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	80.82	gold quality
ganglionic eminence	UBERON:0004023	79.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.50	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.95	gold quality
Brodmann (1909) area 23	UBERON:0013554	77.31	silver quality
buccal mucosa cell	CL:0002336	77.17	gold quality
ventricular zone	UBERON:0003053	77.05	gold quality
cortical plate	UBERON:0005343	74.81	gold quality
oviduct epithelium	UBERON:0004804	73.08	gold quality
middle temporal gyrus	UBERON:0002771	72.60	silver quality
primary visual cortex	UBERON:0002436	71.94	gold quality
occipital lobe	UBERON:0002021	67.52	gold quality
right lobe of thyroid gland	UBERON:0001119	65.63	gold quality
thyroid gland	UBERON:0002046	65.38	gold quality
left lobe of thyroid gland	UBERON:0001120	64.81	gold quality
prefrontal cortex	UBERON:0000451	64.71	gold quality
right lobe of liver	UBERON:0001114	64.31	gold quality
placenta	UBERON:0001987	63.40	gold quality
right adrenal gland	UBERON:0001233	63.39	gold quality
liver	UBERON:0002107	63.28	gold quality
testis	UBERON:0000473	63.23	gold quality
pigmented layer of retina	UBERON:0001782	62.94	silver quality
left adrenal gland	UBERON:0001234	62.81	gold quality
right adrenal gland cortex	UBERON:0035827	62.77	gold quality
ovary	UBERON:0000992	62.76	gold quality
smooth muscle tissue	UBERON:0001135	62.74	gold quality
left adrenal gland cortex	UBERON:0035825	62.63	gold quality
adrenal tissue	UBERON:0018303	62.62	gold quality
neocortex	UBERON:0001950	62.47	gold quality
frontal cortex	UBERON:0001870	62.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

198 targeting SKIDA1, 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-4682	100.00	68.89	1258
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-570-3P	99.96	72.41	4910
HSA-LET-7D-5P	99.96	71.76	1632

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Skida1	ENSMUSG00000054074
rattus_norvegicus	Skida1	ENSRNOG00000033330

Paralogs (2): SIMC1 (ENSG00000170085), EPOP (ENSG00000273604)

Protein

Protein identifiers

SKI/DACH domain-containing protein 1 — Q1XH10 (reviewed: Q1XH10)

Alternative names: Protein DLN-1

All UniProt accessions (1): Q1XH10

UniProt curated annotations — full annotation on UniProt →

Polymorphism. The poly-Ala region of SKIDA1 is highly polymorphic and the number of Ala can vary.

Similarity. Belongs to the DACH/dachshund family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q1XH10-1	1	yes
Q1XH10-2	2

RefSeq proteins (1): NP_997254* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003380	SKI/SNO/DAC	Domain
IPR009061	DNA-bd_dom_put_sf	Homologous_superfamily
IPR027971	EPOP	Family
IPR037000	Ski_DNA-bd_sf	Homologous_superfamily
IPR052119	ElonginBC-PRC2_ViralRestrict	Family

Pfam: PF02437, PF15223

UniProt features (16 total): compositionally biased region 6, sequence conflict 4, region of interest 3, chain 1, cross-link 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q1XH10-F1	49.81	0.10

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 (1): 688

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 247 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, MYAATNNNNNNNGGC_UNKNOWN, AP1_01, FREAC2_01, TAATAAT_MIR126, TGCACTT_MIR519C_MIR519B_MIR519A, GCANCTGNY_MYOD_Q6, AREB6_01, CHX10_01, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, CEBPB_01, AGGCACT_MIR5153P, AP1_Q4_01, FREAC3_01

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (1): DNA-binding transcription factor activity (GO:0003700)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1

Protein interactions and networks

STRING

810 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SKIDA1	FSTL3	O95633	490
SKIDA1	CEP44	Q9C0F1	483
SKIDA1	IKZF2	Q9UKS7	464
SKIDA1	RIOX1	Q9H6W3	460
SKIDA1	RASSF3	Q86WH2	425
SKIDA1	MTF2	Q9Y483	415
SKIDA1	AEBP2	Q6ZN18	413
SKIDA1	UBE2QL1	A1L167	413
SKIDA1	RBMX2	Q9Y388	410
SKIDA1	MLLT10	P55197	396
SKIDA1	DNAJC1	Q96KC8	392
SKIDA1	BMI1	P35226	389
SKIDA1	R4GMX3	R4GMX3	389
SKIDA1	VWC2L	B2RUY7	383
SKIDA1	FBXO8	Q9NRD0	381

IntAct

5 interactions, top by confidence:

A	B	Type	Score
SUZ12	EPOP	psi-mi:“MI:0914”(association)	0.640
EZH1	EPOP	psi-mi:“MI:0914”(association)	0.530
SKIDA1	THAP12	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): SKIDA1 (Affinity Capture-MS), SKIDA1 (Affinity Capture-MS), SUZ12 (Affinity Capture-MS), MTF2 (Affinity Capture-MS), ZNF445 (Affinity Capture-MS), EED (Affinity Capture-MS), PRKRIR (Affinity Capture-MS), EZH2 (Affinity Capture-MS), AGAP3 (Affinity Capture-MS), PHF19 (Affinity Capture-MS), SKIDA1 (Affinity Capture-MS), SKIDA1 (Cross-Linking-MS (XL-MS)), SKIDA1 (Affinity Capture-MS), SKIDA1 (Affinity Capture-RNA)

ESM2 similar proteins: A7X8C7, A7XW20, A7XW25, A9L937, B0VXK3, D4A218, F1MRW8, O00257, O35137, O43248, O43364, O55187, O95503, P06401, P23683, P31270, P31311, P31313, P49640, P59598, P78412, P78413, P82976, Q01822, Q08727, Q1XH10, Q32MQ0, Q4LAL6, Q5TGY3, Q5VZB9, Q60688, Q62414, Q63689, Q6PAL7, Q80YR3, Q8BG36, Q8BZ97, Q8CFG4, Q8NCN4, Q8WNV5

Diamond homologs: A6NHQ4, Q1XH10, Q7TNS8, Q80YR3, H2KY91, Q925Q8, Q96NX9, Q9QYB2, Q9UI36

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	145
Likely benign	11
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

661 predictions. Top by Δscore:

Variant	Effect	Δscore
10:21519071:A:AC	donor_gain	0.9900
10:21519072:C:CC	donor_gain	0.9900
10:21521387:A:AC	donor_gain	0.9900
10:21521388:C:CG	donor_gain	0.9900
10:21521388:CTTTG:C	donor_gain	0.9900
10:21521476:TGACT:T	acceptor_gain	0.9900
10:21521479:CT:C	acceptor_gain	0.9900
10:21521481:C:CC	acceptor_gain	0.9900
10:21523677:GCCTA:G	donor_loss	0.9900
10:21523678:CCTA:C	donor_loss	0.9900
10:21523679:CTAC:C	donor_loss	0.9900
10:21523680:TACCT:T	donor_loss	0.9900
10:21523702:A:AC	donor_gain	0.9900
10:21523703:C:CC	donor_gain	0.9900
10:21523706:AAAT:A	donor_gain	0.9900
10:21523872:C:CC	acceptor_gain	0.9900
10:21521383:ACTT:A	donor_loss	0.9800
10:21521384:CTT:C	donor_loss	0.9800
10:21521384:CTTA:C	donor_gain	0.9800
10:21521385:TTA:T	donor_loss	0.9800
10:21521386:TAC:T	donor_loss	0.9800
10:21521387:ACTT:A	donor_loss	0.9800
10:21521388:CT:C	donor_gain	0.9700
10:21521388:CTTT:C	donor_gain	0.9700
10:21521478:ACTC:A	acceptor_loss	0.9700
10:21521480:TCTAC:T	acceptor_loss	0.9700
10:21521481:C:CA	acceptor_loss	0.9700
10:21521482:T:A	acceptor_loss	0.9700
10:21523868:GAAC:G	acceptor_gain	0.9700
10:21523870:AC:A	acceptor_gain	0.9700

AlphaMissense

5938 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:21515114:G:C	F903L	1.000
10:21515114:G:T	F903L	1.000
10:21515116:A:G	F903L	1.000
10:21515159:C:A	W888C	1.000
10:21515159:C:G	W888C	1.000
10:21515161:A:G	W888R	1.000
10:21515161:A:T	W888R	1.000
10:21515256:A:G	L856P	1.000
10:21516425:G:C	F466L	1.000
10:21516425:G:T	F466L	1.000
10:21516426:A:G	F466S	1.000
10:21516427:A:G	F466L	1.000
10:21517551:A:G	L91P	1.000
10:21517551:A:T	L91H	1.000
10:21517575:A:C	I83S	1.000
10:21517575:A:T	I83N	1.000
10:21517578:A:G	L82P	1.000
10:21517578:A:T	L82H	1.000
10:21517583:G:C	C80W	1.000
10:21517585:A:G	C80R	1.000
10:21517623:A:G	L67P	1.000
10:21517632:A:G	L64S	1.000
10:21517648:A:G	C59R	1.000
10:21517668:A:G	L52P	1.000
10:21517681:G:T	R48S	1.000
10:21517713:A:G	L37P	1.000
10:21517716:A:G	L36P	1.000
10:21517724:G:C	F33L	1.000
10:21517724:G:T	F33L	1.000
10:21517725:A:G	F33S	1.000

dbSNP variants (sampled 300 via entrez): RS1000168078 (10:21522399 A>T), RS1000332314 (10:21516838 C>G,T), RS1000460722 (10:21525723 G>A), RS1000768811 (10:21524169 G>A), RS1000832887 (10:21525437 G>A), RS1000890909 (10:21518553 A>ACCGCACC), RS1001201043 (10:21524386 A>G), RS1001382559 (10:21526446 G>A,C,T), RS1001415145 (10:21526698 T>C), RS1001501197 (10:21524600 G>A,C,T), RS1001615597 (10:21524389 G>C), RS1001956174 (10:21525772 TG>T,TGG), RS1002119945 (10:21518991 G>T), RS1002306665 (10:21520797 G>A), RS1002407080 (10:21519185 G>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

15 associations (top):

Study	Trait	p-value
GCST001941_14	Ovarian cancer	2.000000e-08
GCST001941_15	Ovarian cancer	1.000000e-07
GCST006912_3	Physical activity (overall physical activity time)	4.000000e-09
GCST010135_27	Oily fish consumption	2.000000e-19
GCST010136_13	Fruit consumption	1.000000e-08
GCST010136_20	Fruit consumption	3.000000e-08
GCST010136_26	Fruit consumption	5.000000e-20
GCST010138_13	Raw vegetable consumption	2.000000e-11
GCST010140_44	Pork consumption	2.000000e-19
GCST010142_54	Fish- and plant-related diet	8.000000e-17
GCST010142_65	Fish- and plant-related diet	5.000000e-11
GCST010142_85	Fish- and plant-related diet	2.000000e-24
GCST010703_303	Brain morphology (MOSTest)	1.000000e-27
GCST012231_102	A body shape index	4.000000e-10
GCST90016668_1	Lung volume	6.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0008002	physical activity measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, decreases methylation	4
trichostatin A	affects cotreatment, decreases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
2-methyl-4-isothiazolin-3-one	increases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Fulvestrant	decreases methylation, affects cotreatment	1
Acetaldehyde	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Lead	affects expression	1
Quercetin	decreases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	increases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1

Clinical trials (associated diseases)

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