SCAND1

Summary

SCAND1 (SCAN domain containing 1, HGNC:10566) is a protein-coding gene on chromosome 20q11.23, encoding SCAN domain-containing protein 1 (P57086). May regulate transcriptional activity.

This gene encodes a SCAN box domain-containing protein. The SCAN domain is a highly conserved, leucine-rich motif of approximately 60 aa originally found within a subfamily of zinc finger proteins. This gene belongs to a family of genes that encode an isolated SCAN domain, but no zinc finger motif. This protein binds to and may regulate the function of the transcription factor myeloid zinc finger 1B. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 51282 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_033630

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10566
Approved symbol	SCAND1
Name	SCAN domain containing 1
Location	20q11.23
Locus type	gene with protein product
Status	Approved
Aliases	SDP1, RAZ1
Ensembl gene	ENSG00000171222
Ensembl biotype	protein_coding
OMIM	610416
Entrez	51282

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000305978, ENST00000373991, ENST00000615116, ENST00000857192

RefSeq mRNA: 3 — MANE Select: NM_033630 NM_001385710, NM_016558, NM_033630

CCDS: CCDS13269

Canonical transcript exons

ENST00000305978 — 2 exons

Exon	Start	End
ENSE00001210841	35954448	35954502
ENSE00003913930	35953624	35954339

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 84.4713 / max 429.0524, expressed in 1825 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
187101	41.4926	1821
187099	37.2198	1818
187098	2.2224	1170
187102	1.6675	1127
187103	0.7225	458
187100	0.7189	437
187104	0.3922	56
187097	0.0355	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	96.66	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.61	gold quality
right adrenal gland	UBERON:0001233	95.77	gold quality
right adrenal gland cortex	UBERON:0035827	95.60	gold quality
left adrenal gland cortex	UBERON:0035825	95.56	gold quality
left adrenal gland	UBERON:0001234	95.51	gold quality
adenohypophysis	UBERON:0002196	95.45	gold quality
right lobe of liver	UBERON:0001114	95.33	gold quality
apex of heart	UBERON:0002098	95.04	gold quality
right uterine tube	UBERON:0001302	95.01	gold quality
adrenal cortex	UBERON:0001235	94.97	gold quality
metanephros cortex	UBERON:0010533	94.73	gold quality
mucosa of stomach	UBERON:0001199	94.68	gold quality
granulocyte	CL:0000094	94.53	gold quality
left coronary artery	UBERON:0001626	94.44	gold quality
lower esophagus mucosa	UBERON:0035834	94.38	gold quality
lower esophagus	UBERON:0013473	94.26	gold quality
lower esophagus muscularis layer	UBERON:0035833	94.26	gold quality
body of stomach	UBERON:0001161	94.21	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.20	gold quality
pituitary gland	UBERON:0000007	94.12	gold quality
coronary artery	UBERON:0001621	94.11	gold quality
left uterine tube	UBERON:0001303	94.04	gold quality
ascending aorta	UBERON:0001496	94.02	gold quality
thoracic aorta	UBERON:0001515	94.01	gold quality
anterior cingulate cortex	UBERON:0009835	93.97	gold quality
cingulate cortex	UBERON:0003027	93.90	gold quality
monocyte	CL:0000576	93.80	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.77	gold quality
transverse colon	UBERON:0001157	93.69	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-HCAD-29	no	134.26
E-CURD-120	no	28.95
E-MTAB-8410	no	3.59
E-GEOD-125970	no	3.09
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
ZNF202	Unknown

miRNA regulators (miRDB)

1 targeting SCAND1, 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-335-3P	99.93	73.36	4958

Literature-anchored findings (GeneRIF, showing 2)

• This result indicates that NY-REN-21 can function either as a homodimer or as a heterodimer with SCAND1. (PMID:16540086)
• SCAND1 Reverses Epithelial-to-Mesenchymal Transition (EMT) and Suppresses Prostate Cancer Growth and Migration. (PMID:36552758)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	plagx	ENSDARG00000036855
danio_rerio	ovol1a	ENSDARG00000076472
danio_rerio	plagl2	ENSDARG00000076657
danio_rerio	ovol1b	ENSDARG00000078256
mus_musculus	Scand1	ENSMUSG00000046229
rattus_norvegicus	Scand1	ENSRNOG00000019987
drosophila_melanogaster	hb	FBGN0001180
drosophila_melanogaster	CG12391	FBGN0033581
caenorhabditis_elegans		WBGENE00001824
caenorhabditis_elegans		WBGENE00003033
caenorhabditis_elegans		WBGENE00012385

Paralogs (29): ZNF446 (ENSG00000083838), REST (ENSG00000084093), ZNF174 (ENSG00000103343), OVOL3 (ENSG00000105261), PLAGL1 (ENSG00000118495), ZSCAN18 (ENSG00000121413), ZNF576 (ENSG00000124444), OVOL2 (ENSG00000125850), PLAGL2 (ENSG00000126003), ZSCAN5A (ENSG00000131848), ZSCAN29 (ENSG00000140265), ZSCAN32 (ENSG00000140987), ZSCAN1 (ENSG00000152467), ZNF18 (ENSG00000154957), ZKSCAN2 (ENSG00000155592), ZNF496 (ENSG00000162714), ZNF202 (ENSG00000166261), ZNF641 (ENSG00000167528), ZNF444 (ENSG00000167685), ZNF274 (ENSG00000171606), ZNF131 (ENSG00000172262), OVOL1 (ENSG00000172818), ZNF518A (ENSG00000177853), ZNF518B (ENSG00000178163), PLAG1 (ENSG00000181690), ZSCAN5B (ENSG00000197213), ZNF770 (ENSG00000198146), PEG3 (ENSG00000198300), ZSCAN5C (ENSG00000204532)

Protein

Protein identifiers

SCAN domain-containing protein 1 — P57086 (reviewed: P57086)

All UniProt accessions (1): P57086

UniProt curated annotations — full annotation on UniProt →

Function. May regulate transcriptional activity.

Subunit / interactions. Interacts with ZNF202.

Subcellular location. Nucleus.

RefSeq proteins (3): NP_001372639, NP_057642, NP_361012* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003309	SCAN_dom	Domain
IPR038269	SCAN_sf	Homologous_superfamily
IPR050916	SCAN-C2H2_zinc_finger	Family

Pfam: PF02023

UniProt features (4 total): chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P57086-F1	72.37	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, AREB6_01, HUMMERICH_MALIGNANT_SKIN_TUMOR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, MODULE_123, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, MODULE_98, chr20q11, DANG_BOUND_BY_MYC, MODULE_114, BENPORATH_MYC_MAX_TARGETS, LU_EZH2_TARGETS_UP, HUANG_GATA2_TARGETS_UP

GO Biological Process (1): positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (1): protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

784 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCAND1	ZSCAN2	Q7Z7L9	510
SCAND1	MZF1	P28698	494
SCAND1	SSNA1	O43805	485
SCAND1	DENND11	A4D1U4	478
SCAND1	ZNF322	Q6U7Q0	464
SCAND1	RABAC1	Q9UI14	462
SCAND1	SARNP	P82979	417
SCAND1	PFKL	P17858	405
SCAND1	DRAP1	Q14919	400
SCAND1	UTP3	Q9NQZ2	396
SCAND1	PEX39	Q5I0X4	394
SCAND1	SDF4	Q9BRK5	379
SCAND1	RPS16	P17008	376
SCAND1	CCDC9	Q9Y3X0	368
SCAND1	COX19	Q49B96	365

IntAct

284 interactions, top by confidence:

A	B	Type	Score
PGBD1	SCAND1	psi-mi:“MI:0915”(physical association)	0.940
SCAND1	PGBD1	psi-mi:“MI:0915”(physical association)	0.940
ZKSCAN4	SCAND1	psi-mi:“MI:0915”(physical association)	0.870
SCAND1	ZKSCAN4	psi-mi:“MI:0915”(physical association)	0.870
ZNF24	SCAND1	psi-mi:“MI:0915”(physical association)	0.850
ZNF263	SCAND1	psi-mi:“MI:0915”(physical association)	0.800
ZSCAN22	SCAND1	psi-mi:“MI:0915”(physical association)	0.760
ZNF394	SCAND1	psi-mi:“MI:0914”(association)	0.740
SCAND1	ZNF394	psi-mi:“MI:0915”(physical association)	0.740
SCAND1	ZSCAN18	psi-mi:“MI:0915”(physical association)	0.740
ZNF449	SCAND1	psi-mi:“MI:0915”(physical association)	0.720
GORASP2	SCAND1	psi-mi:“MI:0915”(physical association)	0.720
SCAND1	ZNF449	psi-mi:“MI:0915”(physical association)	0.720
SCAND1	GORASP2	psi-mi:“MI:0915”(physical association)	0.720
ZNF396	ZNF24	psi-mi:“MI:0914”(association)	0.700
SCAND1	ZKSCAN7	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (117): SCAND1 (Two-hybrid), SCAND1 (Two-hybrid), ZKSCAN7 (Two-hybrid), PGBD1 (Two-hybrid), ZNF449 (Two-hybrid), ZKSCAN4 (Two-hybrid), SCAND1 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), SCAND1 (Two-hybrid), ZSCAN32 (Two-hybrid), ZKSCAN7 (Two-hybrid)

ESM2 similar proteins: A1YEW3, A1YG31, A2T715, A2T7M0, A6NEV1, A6NGD5, A6NJL1, A6QPT6, A8MXV6, A8MZF0, A8WFF7, O08664, P03327, P06936, P0C6A0, P0DPQ3, P54257, P57086, P86478, P86479, P86480, P86481, P86496, Q13487, Q32PG5, Q505G4, Q5R7P6, Q68FX5, Q6J1H4, Q6NZN1, Q6ZMS7, Q6ZRT6, Q76NI1, Q7L3V2, Q7TPK6, Q7YR42, Q7Z6I6, Q80UE6, Q8IY33, Q8K2W9

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YEW3, A1YFW2, A1YFW6, A1YG26, A1YG31, A1YG48, A1YG60, A1YGJ4, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T715, A2T736, A2T7D2, A2T7D7, A2T7F4, A2T7L7, A2T7M0, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P17022, P17028, P17029, P17040, P28698, P49910, P51815

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SCAND1	“up-regulates activity”	MZF1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

78 predictions. Top by Δscore:

Variant	Effect	Δscore
20:35954442:GCTTA:G	donor_loss	0.9900
20:35954443:CTTA:C	donor_loss	0.9900
20:35954444:TTA:T	donor_loss	0.9900
20:35954445:TACC:T	donor_loss	0.9900
20:35954446:A:AG	donor_loss	0.9900
20:35954447:C:CA	donor_loss	0.9900
20:35954449:TGC:T	donor_gain	0.9300
20:35954441:AGCTT:A	donor_loss	0.9100
20:35954446:A:AC	donor_gain	0.9100
20:35954447:C:CC	donor_gain	0.9100
20:35954340:C:CC	acceptor_gain	0.8600
20:35954350:G:GC	acceptor_gain	0.8600
20:35954343:C:CT	acceptor_gain	0.8300
20:35954350:G:C	acceptor_gain	0.8300
20:35954375:G:T	acceptor_gain	0.8200
20:35954447:CCTG:C	donor_gain	0.8200
20:35954346:G:T	acceptor_gain	0.7900
20:35954360:C:CT	acceptor_gain	0.7800
20:35954338:GTC:G	acceptor_loss	0.7700
20:35954339:TCTG:T	acceptor_loss	0.7700
20:35954340:CTGC:C	acceptor_loss	0.7700
20:35954337:CGT:C	acceptor_gain	0.7500
20:35954345:C:CT	acceptor_gain	0.7400
20:35954355:G:GC	acceptor_gain	0.7200
20:35954339:TCTGC:T	acceptor_gain	0.6900
20:35954340:C:A	acceptor_gain	0.6900
20:35954355:G:C	acceptor_gain	0.6900
20:35954447:CCT:C	donor_gain	0.6900
20:35954448:CTG:C	donor_gain	0.6800
20:35954341:T:G	acceptor_gain	0.6600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000417733 (20:35954855 C>A,T), RS1000532386 (20:35955180 C>G,T), RS1000623838 (20:35955404 A>C,T), RS1001208966 (20:35961397 G>A,T), RS1001681897 (20:35954673 G>A,C), RS1001734465 (20:35954860 G>A,C,T), RS1002087003 (20:35956285 C>T), RS1002203138 (20:35956686 A>G), RS1002366268 (20:35961017 C>T), RS1002826552 (20:35959235 A>G,T), RS1003037227 (20:35953843 C>A,G,T), RS1003403803 (20:35953623 A>G,T), RS1003579574 (20:35959563 T>C), RS1004563910 (20:35957729 A>G), RS1004575207 (20:35953130 A>T)

Disease associations

OMIM: gene MIM:610416 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004067_1	Hip circumference adjusted for BMI	1.000000e-07
GCST004067_136	Hip circumference adjusted for BMI	8.000000e-07
GCST004067_92	Hip circumference adjusted for BMI	6.000000e-12
GCST010002_66	Refractive error	2.000000e-20

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Estradiol	increases reaction, decreases expression, affects binding	2
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
ICG 001	decreases expression	1
abrine	increases expression	1
(+)-JQ1 compound	decreases expression	1
MT19c compound	decreases expression	1
Decitabine	increases expression	1
Caffeine	increases phosphorylation	1
Dimethylnitrosamine	decreases expression	1
Hydrogen Peroxide	affects expression	1
Methotrexate	decreases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Valproic Acid	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	decreases expression	1
Phenol	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	increases abundance, decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2EN	Abcam HeLa SCAND1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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