SCP2D1

Summary

SCP2D1 (SCP2 sterol binding domain containing 1, HGNC:16211) is a protein-coding gene on chromosome 20p11.23, encoding SCP2 sterol-binding domain-containing protein 1 (Q9UJQ7).

Predicted to be active in cytosol.

Source: NCBI Gene 140856 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_178483

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16211
Approved symbol	SCP2D1
Name	SCP2 sterol binding domain containing 1
Location	20p11.23
Locus type	gene with protein product
Status	Approved
Aliases	dJ1068E13.2, HSD22
Ensembl gene	ENSG00000132631
Ensembl biotype	protein_coding
Entrez	140856

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000377428

RefSeq mRNA: 1 — MANE Select: NM_178483 NM_178483

CCDS: CCDS13139

Canonical transcript exons

ENST00000377428 — 1 exons

Exon	Start	End
ENSE00001473882	18813783	18814378

Expression profiles

Bgee: expression breadth broad, 23 present calls, max score 95.68.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0266 / max 23.9075, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
183700	0.0266	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.68	gold quality
left testis	UBERON:0004533	93.40	gold quality
right testis	UBERON:0004534	93.18	gold quality
testis	UBERON:0000473	90.39	gold quality
sperm	CL:0000019	90.36	gold quality
adult organism	UBERON:0007023	75.31	gold quality
pancreatic ductal cell	CL:0002079	62.28	silver quality
tibialis anterior	UBERON:0001385	61.27	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	55.58	gold quality
epithelial cell of pancreas	CL:0000083	54.93	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
deltoid	UBERON:0001476	52.04	gold quality
ileal mucosa	UBERON:0000331	51.09	silver quality
myocardium	UBERON:0002349	50.25	gold quality
upper leg skin	UBERON:0004262	49.02	silver quality
quadriceps femoris	UBERON:0001377	47.17	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
middle temporal gyrus	UBERON:0002771	45.77	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
sural nerve	UBERON:0015488	44.34	silver quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
trachea	UBERON:0003126	42.31	gold quality
muscle tissue	UBERON:0002385	41.58	gold quality
skeletal muscle tissue	UBERON:0001134	41.55	gold quality
lower esophagus mucosa	UBERON:0035834	41.37	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting SCP2D1, 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-548C-3P	99.99	74.01	7587
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-22-5P	97.67	68.92	1355
HSA-MIR-6869-5P	97.17	67.06	634
HSA-MIR-136-3P	93.27	66.31	131

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Scp2d1	ENSMUSG00000027431
rattus_norvegicus	Scp2d1	ENSRNOG00000009461
drosophila_melanogaster	ScpX	FBGN0015808

Paralogs (1): SCP2 (ENSG00000116171)

Protein

Protein identifiers

SCP2 sterol-binding domain-containing protein 1 — Q9UJQ7 (reviewed: Q9UJQ7)

All UniProt accessions (1): Q9UJQ7

RefSeq proteins (1): NP_848578* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003033	SCP2_sterol-bd_dom	Domain
IPR036527	SCP2_sterol-bd_dom_sf	Homologous_superfamily

Pfam: PF02036

UniProt features (3 total): chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UJQ7-F1	82.32	0.67

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): TCF4_Q5, ATF1_Q6, TGACATY_UNKNOWN, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, TGGAAA_NFAT_Q4_01, chr20p11, CDC5_01, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_UP, MIR6869_5P, GSE13306_RA_VS_UNTREATED_TCONV_DN, MIR136_3P, ACAWYAAAG_UNKNOWN, GSE15659_CD45RA_NEG_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_ACTIVATED_TREG_UP, GSE15659_RESTING_TREG_VS_NONSUPPRESSIVE_TCELL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1036 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCP2D1	FNDC8	Q8TC99	665
SCP2D1	IDNK	Q5T6J7	543
SCP2D1	STOML1	Q9UBI4	524
SCP2D1	CIMIP4	O43247	507
SCP2D1	SPATA31D1	Q6ZQQ2	482
SCP2D1	NOCT	Q9UK39	453
SCP2D1	LYZL6	O75951	447
SCP2D1	ACTL9	Q8TC94	419
SCP2D1	NTAN1	Q96AB6	403
SCP2D1	TMEM202	A6NGA9	370
SCP2D1	HMGB4	Q8WW32	364
SCP2D1	LHFPL3	Q86UP9	359
SCP2D1	FAM221B	A6H8Z2	356
SCP2D1	SPZ1	Q9BXG8	352
SCP2D1	PDE7B	Q9NP56	347

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SCP2D1	EHD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): EHD3 (Affinity Capture-MS), EHD1 (Affinity Capture-MS)

ESM2 similar proteins: A1YVX4, A2VDN5, A2VDR2, A7T395, B7FF67, B7PXE3, B7ZC32, D3YXS5, F8WLE0, O43150, O77775, P19878, P34550, P49589, Q01H90, Q05AS3, Q0P561, Q2TBS3, Q3V3R1, Q5F414, Q5RJK8, Q5U243, Q62082, Q6AZT2, Q6DDB9, Q6PGC1, Q6VBQ6, Q6VBQ8, Q6VEU3, Q6XL73, Q717R8, Q719I0, Q719N1, Q7SIG6, Q7XUR2, Q7YRD0, Q8C9X1, Q8CIG3, Q8NB78, Q8SS49

Diamond homologs: A0A384E138, A4FUZ6, A6TGM3, B5FEW7, G5EDP2, O26884, O62742, P07857, P11915, P22009, P22307, P32020, P51659, P51660, P73825, P80547, P97852, Q00680, Q05493, Q07598, Q23655, Q2TBS3, Q2TPA8, Q39VG1, Q4V8F9, Q5E8X7, Q5RA68, Q66KC4, Q6P5L8, Q6PAY8, Q6YN16, Q8CI66, Q9DAH1, Q9FMN0, Q9KJF3, Q9NKW1, Q9UBI4, Q9UJQ7, P07871, P21775

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

94 predictions. Top by Δscore:

Variant	Effect	Δscore
20:18813963:GACAT:G	donor_gain	0.8600
20:18813984:G:GT	donor_gain	0.8400
20:18814049:G:T	donor_gain	0.8000
20:18814049:G:GT	donor_gain	0.7700
20:18814211:A:T	donor_gain	0.7300
20:18813885:GTTC:G	donor_gain	0.7000
20:18813886:TTCT:T	donor_gain	0.7000
20:18814221:G:GG	donor_gain	0.6600
20:18813872:GGGCC:G	donor_gain	0.6300
20:18813858:G:GT	donor_gain	0.6200
20:18814003:TC:T	donor_gain	0.6100
20:18813887:TCTG:T	donor_gain	0.6000
20:18813888:CTGG:C	donor_gain	0.5800
20:18814215:TTCA:T	donor_gain	0.5700
20:18813812:G:GT	donor_gain	0.5300
20:18814008:A:T	donor_gain	0.5300
20:18814217:CAAAG:C	donor_loss	0.5200
20:18814218:AAAGT:A	donor_loss	0.5200
20:18814219:AAG:A	donor_loss	0.5200
20:18814222:T:TC	donor_loss	0.5200
20:18814224:A:AC	donor_loss	0.5200
20:18814229:C:T	donor_gain	0.5200
20:18813929:GCT:G	donor_gain	0.5100
20:18814219:AA:A	donor_gain	0.5100
20:18814216:TCAAA:T	donor_gain	0.5000
20:18814225:G:C	donor_loss	0.5000
20:18813873:G:A	donor_gain	0.4900
20:18814148:G:GT	donor_gain	0.4900
20:18814066:G:GA	donor_gain	0.4700
20:18813826:G:GT	donor_gain	0.4600

AlphaMissense

1031 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:18814023:T:C	F70L	0.937
20:18814025:T:A	F70L	0.937
20:18814025:T:G	F70L	0.937
20:18814200:T:C	F129L	0.933
20:18814202:C:A	F129L	0.933
20:18814202:C:G	F129L	0.933
20:18814242:A:C	S143R	0.918
20:18814244:C:A	S143R	0.918
20:18814244:C:G	S143R	0.918
20:18814024:T:C	F70S	0.917
20:18814030:T:C	L72P	0.914
20:18814078:T:C	L88P	0.909
20:18814017:G:C	A68P	0.906
20:18814138:T:C	F108S	0.899
20:18814168:T:C	L118P	0.879
20:18814228:G:T	G138V	0.877
20:18814072:T:A	I86N	0.876
20:18814137:T:C	F108L	0.858
20:18814139:T:A	F108L	0.858
20:18814139:T:G	F108L	0.858
20:18814216:T:C	F134S	0.857
20:18814065:T:A	W84R	0.854
20:18814065:T:C	W84R	0.854
20:18814030:T:G	L72R	0.850
20:18814201:T:C	F129S	0.846
20:18814027:A:C	Q71P	0.839
20:18814144:T:C	I110T	0.837
20:18814144:T:A	I110N	0.828
20:18814030:T:A	L72Q	0.813
20:18814210:G:T	G132V	0.813

dbSNP variants (sampled 300 via entrez): RS1000645701 (20:18813488 A>G), RS1000709317 (20:18814507 T>C), RS1000782543 (20:18813068 G>A), RS1001933043 (20:18814505 C>CT), RS1001985780 (20:18813093 G>T), RS1003872423 (20:18814559 C>T), RS1004739016 (20:18814669 T>C), RS1004880114 (20:18813126 G>T), RS1004976369 (20:18813392 C>T), RS1009067130 (20:18811953 G>A), RS1009354313 (20:18812907 C>T), RS1010360044 (20:18814211 A>C,G), RS1013263735 (20:18813650 G>A,C), RS1014251910 (20:18814608 T>C), RS1014316104 (20:18812372 A>G)

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

3 associations (top):

Study	Trait	p-value
GCST002248_3	Fasting insulin (dietary factor interaction)	2.000000e-06
GCST002253_15	Homeostasis model assessment of insulin resistance (dietary factor interaction)	5.000000e-06
GCST004860_57	Alcoholic chronic pancreatitis	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004501	HOMA-IR

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation	1
Cyclosporine	increases methylation	1

Clinical trials (associated diseases)

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