SCRN3

Summary

SCRN3 (secernin 3, HGNC:30382) is a protein-coding gene on chromosome 2q31.1, encoding Secernin-3 (Q0VDG4). Plays a role in thermal nociception.

Predicted to enable cysteine-type exopeptidase activity and dipeptidase activity. Predicted to be involved in detection of temperature stimulus involved in sensory perception of pain.

Source: NCBI Gene 79634 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 65 total
• Druggable target: yes
• MANE Select transcript: NM_024583

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30382
Approved symbol	SCRN3
Name	secernin 3
Location	2q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23142
Ensembl gene	ENSG00000144306
Ensembl biotype	protein_coding
OMIM	614967
Entrez	79634

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 18 protein_coding, 5 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000272732, ENST00000409673, ENST00000424069, ENST00000427038, ENST00000435964, ENST00000437944, ENST00000458563, ENST00000475928, ENST00000488349, ENST00000490927, ENST00000548031, ENST00000548868, ENST00000548921, ENST00000549848, ENST00000877601, ENST00000877602, ENST00000877603, ENST00000877604, ENST00000877605, ENST00000877606, ENST00000877607, ENST00000877608, ENST00000968051, ENST00000968052, ENST00000968053

RefSeq mRNA: 11 — MANE Select: NM_024583 NM_001193528, NM_001412202, NM_001412203, NM_001412204, NM_001412205, NM_001412206, NM_001412207, NM_001412208, NM_001412209, NM_001412210, NM_024583

CCDS: CCDS2258, CCDS54420

Canonical transcript exons

ENST00000272732 — 8 exons

Exon	Start	End
ENSE00001016386	174398275	174398442
ENSE00001710210	174395730	174395817
ENSE00002362279	174427713	174429575
ENSE00003463596	174424475	174424649
ENSE00003488885	174404103	174404315
ENSE00003670993	174400990	174401189
ENSE00003678766	174422885	174423047
ENSE00003784643	174399922	174400103

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 91.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.3139 / max 332.3969, expressed in 1780 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
23792	13.9174	1757
23793	0.7657	403
23794	0.6309	370

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	91.35	gold quality
ganglionic eminence	UBERON:0004023	90.93	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.73	gold quality
ventricular zone	UBERON:0003053	90.24	gold quality
esophagus squamous epithelium	UBERON:0006920	89.69	gold quality
spinal cord	UBERON:0002240	89.29	gold quality
islet of Langerhans	UBERON:0000006	89.24	gold quality
adrenal tissue	UBERON:0018303	89.12	gold quality
prefrontal cortex	UBERON:0000451	89.06	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.66	gold quality
calcaneal tendon	UBERON:0003701	88.51	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.37	gold quality
jejunal mucosa	UBERON:0000399	88.29	gold quality
rectum	UBERON:0001052	87.69	gold quality
muscle of leg	UBERON:0001383	87.62	gold quality
oral cavity	UBERON:0000167	87.42	gold quality
monocyte	CL:0000576	87.32	gold quality
gastrocnemius	UBERON:0001388	87.22	gold quality
anterior cingulate cortex	UBERON:0009835	87.12	gold quality
mononuclear cell	CL:0000842	86.98	gold quality
cingulate cortex	UBERON:0003027	86.98	gold quality
right adrenal gland cortex	UBERON:0035827	86.76	gold quality
right adrenal gland	UBERON:0001233	86.70	gold quality
amygdala	UBERON:0001876	86.60	gold quality
biceps brachii	UBERON:0001507	86.57	gold quality
leukocyte	CL:0000738	86.52	gold quality
palpebral conjunctiva	UBERON:0001812	86.25	gold quality
jejunum	UBERON:0002115	86.19	gold quality
tonsil	UBERON:0002372	86.18	gold quality
eye	UBERON:0000970	86.17	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.55
E-MTAB-6075	no	1552.17
E-GEOD-99795	no	70.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting SCRN3, 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-5011-5P	100.00	83.46	5820
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-4255	99.72	67.70	1541
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-33A-3P	99.70	70.27	3362

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	scrn3	ENSDARG00000016611
mus_musculus	Scrn3	ENSMUSG00000008226
rattus_norvegicus	Scrn3	ENSRNOG00000018657
drosophila_melanogaster	CG10098	FBGN0037472

Paralogs (2): SCRN1 (ENSG00000136193), SCRN2 (ENSG00000141295)

Protein

Protein identifiers

Secernin-3 — Q0VDG4 (reviewed: Q0VDG4)

All UniProt accessions (7): Q0VDG4, A0A1D5RMN9, C9JID8, C9JNS3, F8W0M9, F8WBX0, H9KVC8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in thermal nociception.

Similarity. Belongs to the peptidase C69 family. Secernin subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q0VDG4-1	1	yes
Q0VDG4-2	2

RefSeq proteins (11): NP_001180457, NP_001399131, NP_001399132, NP_001399133, NP_001399134, NP_001399135, NP_001399136, NP_001399137, NP_001399138, NP_001399139, NP_078859* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005322	Peptidase_C69	Family

Pfam: PF03577

UniProt features (10 total): sequence variant 3, modified residue 2, propeptide 1, chain 1, active site 1, splice variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q0VDG4-F1	91.96	0.81

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 6

Post-translational modifications (2): 6, 6

Mutagenesis-validated functional residues (1):

Position	Phenotype
2–5	does not affect glyoxylate or pyruvate formation.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 115 (showing top): FREAC2_01, GOBP_SENSORY_PERCEPTION_OF_TEMPERATURE_STIMULUS, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, FOXO1_01, GOBP_SENSORY_PERCEPTION_OF_PAIN, GOBP_DETECTION_OF_TEMPERATURE_STIMULUS, FREAC3_01, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, FOXO4_02

GO Biological Process (2): proteolysis (GO:0006508), detection of temperature stimulus involved in sensory perception of pain (GO:0050965)

GO Molecular Function (2): dipeptidase activity (GO:0016805), cysteine-type exopeptidase activity (GO:0070004)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
exopeptidase activity	2
protein metabolic process	1
sensory perception of pain	1
detection of temperature stimulus involved in sensory perception	1
cysteine-type peptidase activity	1

Protein interactions and networks

STRING

578 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCRN3	ZNF639	Q9UID6	414
SCRN3	ZNF227	Q86WZ6	398
SCRN3	ASB8	Q9H765	397
SCRN3	ALKBH1	Q13686	394
SCRN3	ADO	Q96SZ5	381
SCRN3	HBM	Q6B0K9	377
SCRN3	CCDC82	Q8N4S0	375
SCRN3	ERGIC2	Q96RQ1	372
SCRN3	ITPRIPL2	Q3MIP1	370
SCRN3	DNAJC16	Q9Y2G8	366
SCRN3	MITD1	Q8WV92	356
SCRN3	SIPA1L3	O60292	342
SCRN3	ST8SIA3	O43173	342
SCRN3	RHBG	Q9H310	339
SCRN3	FAM76B	Q5HYJ3	336

IntAct

16 interactions, top by confidence:

A	B	Type	Score
MAGOH	CASC3	psi-mi:“MI:0914”(association)	0.970
SMYD1	ADSS2	psi-mi:“MI:0914”(association)	0.780
DYDC2	INPPL1	psi-mi:“MI:0914”(association)	0.560
RCVRN	RAB9A	psi-mi:“MI:0914”(association)	0.530
SCRN3	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
SCRN3	EPS8	psi-mi:“MI:0915”(physical association)	0.440
EPS8	SCRN3	psi-mi:“MI:0403”(colocalization)	0.440
SPATA20	SCRN3	psi-mi:“MI:0914”(association)	0.350
MAPK1	SPAG9	psi-mi:“MI:0914”(association)	0.350
PID1	LRPAP1	psi-mi:“MI:0914”(association)	0.350
SPATA20	HDAC4	psi-mi:“MI:0914”(association)	0.350
SCRN3	OXSR1	psi-mi:“MI:0914”(association)	0.350

BioGRID (27): SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Reconstituted Complex), SCRN3 (Affinity Capture-RNA), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), SCRN3 (Affinity Capture-MS), OXSR1 (Affinity Capture-MS)

ESM2 similar proteins: A2VD33, A7SLW1, A9RBS1, B4G0F3, B8BKI7, C6JS30, E0CTF3, F4IV16, K7QHS5, K7QKH1, O00116, O15382, O22494, O23617, O23732, O35854, O35855, O80738, P0C7R2, P24288, P46416, P54687, P54688, P54690, P97275, Q06429, Q0VDG4, Q0WUI9, Q28C69, Q3T056, Q5EA40, Q5R979, Q5REP0, Q6PCE3, Q8C0I1, Q8L7M0, Q93Y32, Q948J9, Q94AH8, Q9FIV6

Diamond homologs: P83939, Q0V984, Q0VDG4, Q12765, Q17QS0, Q3TMH2, Q5TYS5, Q5XH17, Q6AY84, Q6AYR8, Q803W1, Q8VCA8, Q96FV2, Q9CZC8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1270 predictions. Top by Δscore:

Variant	Effect	Δscore
2:174398273:A:AG	acceptor_gain	1.0000
2:174398274:G:GG	acceptor_gain	1.0000
2:174398301:T:TA	acceptor_gain	1.0000
2:174398438:TTAAG:T	donor_loss	1.0000
2:174398439:TAAG:T	donor_loss	1.0000
2:174398443:G:A	donor_loss	1.0000
2:174398444:T:G	donor_loss	1.0000
2:174399919:CA:C	acceptor_loss	1.0000
2:174399920:A:AG	acceptor_gain	1.0000
2:174399920:AGT:A	acceptor_gain	1.0000
2:174399921:G:GA	acceptor_gain	1.0000
2:174399921:GT:G	acceptor_gain	1.0000
2:174399921:GTG:G	acceptor_gain	1.0000
2:174399921:GTGT:G	acceptor_gain	1.0000
2:174399921:GTGTA:G	acceptor_gain	1.0000
2:174400075:G:GT	donor_gain	1.0000
2:174400088:G:GT	donor_gain	1.0000
2:174400089:A:T	donor_gain	1.0000
2:174400099:GTCAG:G	donor_loss	1.0000
2:174400100:TCAG:T	donor_loss	1.0000
2:174400101:CAGGT:C	donor_loss	1.0000
2:174400102:AGGTT:A	donor_loss	1.0000
2:174400988:A:AG	acceptor_gain	1.0000
2:174400989:G:GG	acceptor_gain	1.0000
2:174400989:GACTT:G	acceptor_gain	1.0000
2:174401161:G:T	donor_gain	1.0000
2:174401187:AAGGT:A	donor_loss	1.0000
2:174401188:AGGT:A	donor_loss	1.0000
2:174401190:GT:G	donor_loss	1.0000
2:174401191:T:G	donor_loss	1.0000

AlphaMissense

2821 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:174398357:A:T	K25I	0.999
2:174398358:A:C	K25N	0.997
2:174398358:A:T	K25N	0.997
2:174422971:A:C	S281R	0.997
2:174422973:C:A	S281R	0.997
2:174422973:C:G	S281R	0.997
2:174398361:T:A	N26K	0.996
2:174398361:T:G	N26K	0.996
2:174398357:A:C	K25T	0.995
2:174398354:G:A	G24E	0.994
2:174399973:A:C	S71R	0.994
2:174399975:T:A	S71R	0.994
2:174399975:T:G	S71R	0.994
2:174400998:T:C	L117P	0.994
2:174398356:A:G	K25E	0.993
2:174422921:G:C	R264P	0.993
2:174399994:G:A	G78R	0.992
2:174399994:G:C	G78R	0.992
2:174399994:G:T	G78W	0.992
2:174400009:G:C	A83P	0.992
2:174400990:A:C	R114S	0.992
2:174400990:A:T	R114S	0.992
2:174400093:G:C	D111H	0.991
2:174422980:T:C	S284P	0.991
2:174398356:A:C	K25Q	0.990
2:174399997:G:C	A79P	0.990
2:174400006:G:A	G82R	0.990
2:174400006:G:C	G82R	0.990
2:174400025:T:A	V88D	0.990
2:174400033:G:T	G91W	0.990

dbSNP variants (sampled 300 via entrez): RS1000053905 (2:174396494 G>A,T), RS1000065902 (2:174421665 A>G), RS1000169259 (2:174400618 G>A), RS1000289039 (2:174402799 C>A), RS1000387836 (2:174395386 C>A), RS1000536436 (2:174414599 A>G), RS1000612020 (2:174400805 C>T), RS1000624054 (2:174410030 G>A), RS1000676112 (2:174410290 T>G), RS1000680131 (2:174402539 T>C), RS1000979648 (2:174421102 A>G), RS1001067100 (2:174423296 A>G), RS1001117208 (2:174413239 C>G,T), RS1001128550 (2:174413858 T>A), RS1001266047 (2:174394982 G>A)

Disease associations

OMIM: gene MIM:614967 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST007953_11	Glycated hemoglobin levels	4.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004541	HbA1c measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6196085 (SINGLE PROTEIN)

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.70	IC50	200	nM	CHEMBL6172043

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
geldanamycin	increases expression	1
methylmercuric chloride	decreases expression	1
trichostatin A	decreases expression	1
beta-lapachone	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
pentanal	decreases expression	1
abrine	decreases expression	1
Vorinostat	increases expression	1
Benzo(a)pyrene	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	increases expression	1
Gallic Acid	decreases expression	1
Manganese	decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Testosterone	decreases expression	1
Thimerosal	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL6136116	Binding	Inhibition of full length human SCRN3 transfected in HEK293T cells	Classifying covalent protein binders by their targeted binding site. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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