SCRN2

Summary

SCRN2 (secernin 2, HGNC:30381) is a protein-coding gene on chromosome 17q21.32, encoding Secernin-2 (Q96FV2).

Predicted to enable cysteine-type exopeptidase activity and dipeptidase activity. Predicted to be involved in proteolysis. Located in extracellular exosome.

Source: NCBI Gene 90507 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_138355

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30381
Approved symbol	SCRN2
Name	secernin 2
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000141295
Ensembl biotype	protein_coding
OMIM	614966
Entrez	90507

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 11 protein_coding, 4 retained_intron, 4 nonsense_mediated_decay

ENST00000290216, ENST00000407215, ENST00000578323, ENST00000578840, ENST00000579856, ENST00000580428, ENST00000581546, ENST00000581645, ENST00000582459, ENST00000582656, ENST00000583090, ENST00000584123, ENST00000584567, ENST00000895877, ENST00000895878, ENST00000895879, ENST00000895880, ENST00000895881, ENST00000928918

RefSeq mRNA: 2 — MANE Select: NM_138355 NM_001145023, NM_138355

CCDS: CCDS11519, CCDS45723

Canonical transcript exons

ENST00000290216 — 8 exons

Exon	Start	End
ENSE00000947505	47840191	47840372
ENSE00001137634	47841208	47841273
ENSE00001194326	47837692	47838002
ENSE00003517439	47838531	47838696
ENSE00003525475	47838791	47839006
ENSE00003538582	47839444	47839643
ENSE00003544857	47840670	47840843
ENSE00003618363	47838270	47838450

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 95.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1075 / max 54.5147, expressed in 1682 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166612	4.5055	1661
166611	0.6020	220

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	95.59	gold quality
right lobe of thyroid gland	UBERON:0001119	95.30	gold quality
right uterine tube	UBERON:0001302	94.88	gold quality
left lobe of thyroid gland	UBERON:0001120	94.80	gold quality
adult mammalian kidney	UBERON:0000082	94.53	gold quality
omental fat pad	UBERON:0010414	93.96	gold quality
peritoneum	UBERON:0002358	93.91	gold quality
metanephros cortex	UBERON:0010533	93.84	gold quality
adipose tissue of abdominal region	UBERON:0007808	93.81	gold quality
adenohypophysis	UBERON:0002196	93.77	gold quality
thyroid gland	UBERON:0002046	93.62	gold quality
subcutaneous adipose tissue	UBERON:0002190	93.58	gold quality
pancreatic ductal cell	CL:0002079	93.19	silver quality
adipose tissue	UBERON:0001013	93.16	gold quality
mucosa of transverse colon	UBERON:0004991	93.16	gold quality
cortex of kidney	UBERON:0001225	93.09	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.09	gold quality
pituitary gland	UBERON:0000007	92.83	gold quality
spleen	UBERON:0002106	92.80	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.75	gold quality
minor salivary gland	UBERON:0001830	92.64	gold quality
kidney epithelium	UBERON:0004819	92.47	gold quality
small intestine	UBERON:0002108	92.17	gold quality
saliva-secreting gland	UBERON:0001044	92.14	gold quality
body of uterus	UBERON:0009853	92.09	gold quality
endocervix	UBERON:0000458	92.07	gold quality
right atrium auricular region	UBERON:0006631	92.06	gold quality
right lobe of liver	UBERON:0001114	91.97	gold quality
transverse colon	UBERON:0001157	91.90	gold quality
cerebellar hemisphere	UBERON:0002245	91.81	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

4 targeting SCRN2, 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-6835-3P	99.93	70.49	2904
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-4709-3P	98.88	68.04	1594

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	scrn2	ENSDARG00000043497
mus_musculus	Scrn2	ENSMUSG00000020877
rattus_norvegicus	Scrn2	ENSRNOG00000010214
drosophila_melanogaster	CG10098	FBGN0037472

Paralogs (2): SCRN1 (ENSG00000136193), SCRN3 (ENSG00000144306)

Protein

Protein identifiers

Secernin-2 — Q96FV2 (reviewed: Q96FV2)

All UniProt accessions (8): A0A384NKK8, Q96FV2, J3KS57, J3KT79, J3QL71, J3QQM9, J3QR84, J3QRJ1

UniProt curated annotations — full annotation on UniProt →

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q96FV2-1	1	yes
Q96FV2-2	2

RefSeq proteins (2): NP_001138495, NP_612364* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005322	Peptidase_C69	Family

Pfam: PF03577

UniProt features (9 total): sequence variant 5, chain 1, active site 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96FV2-F1	94.68	0.90

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): 12

Post-translational modifications (1): 52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, SANSOM_APC_MYC_TARGETS, GOBP_PROTEOLYSIS, GOMF_PEPTIDASE_ACTIVITY, GOMF_DIPEPTIDASE_ACTIVITY, GOMF_EXOPEPTIDASE_ACTIVITY, DODD_NASOPHARYNGEAL_CARCINOMA_DN, SRC_UP.V1_DN, GSE14415_ACT_TCONV_VS_ACT_NATURAL_TREG_UP, GOMF_CYSTEINE_TYPE_EXOPEPTIDASE_ACTIVITY, CBX5_TARGET_GENES, RYBP_TARGET_GENES, ZNF2_TARGET_GENES, ZNF423_TARGET_GENES, MIR6835_3P

GO Biological Process (1): proteolysis (GO:0006508)

GO Molecular Function (3): dipeptidase activity (GO:0016805), cysteine-type exopeptidase activity (GO:0070004), protein binding (GO:0005515)

GO Cellular Component (1): extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
exopeptidase activity	2
protein metabolic process	1
cysteine-type peptidase activity	1
binding	1
extracellular vesicle	1

Protein interactions and networks

STRING

696 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCRN2	LRRC46	Q96FV0	400
SCRN2	CEP128	Q6ZU80	399
SCRN2	NMRAL1	Q9HBL8	397
SCRN2	CEP152	O94986	389
SCRN2	ABHD14B	Q96IU4	384
SCRN2	PRRC2C	Q9Y520	373
SCRN2	NXPH2	O95156	372
SCRN2	ORMDL2	Q53FV1	370
SCRN2	PRR15L	Q9BU68	365
SCRN2	SNX11	Q9Y5W9	362
SCRN2	SNX32	Q86XE0	349
SCRN2	SLC39A5	Q6ZMH5	347
SCRN2	DNASE2	O00115	346
SCRN2	OSBPL7	Q9BZF2	337
SCRN2	PIPOX	Q9P0Z9	328

IntAct

24 interactions, top by confidence:

A	B	Type	Score
NFKBIA	POLRMT	psi-mi:“MI:0914”(association)	0.670
PEX5	SCRN2	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	SCRN2	psi-mi:“MI:0915”(physical association)	0.560
KAT5	SCRN2	psi-mi:“MI:0915”(physical association)	0.560
SOX2	PDLIM1	psi-mi:“MI:0914”(association)	0.530
TAS2R41	YKT6	psi-mi:“MI:0914”(association)	0.530
MARCKSL1	NMT2	psi-mi:“MI:0914”(association)	0.530
DBF4B	CDC7	psi-mi:“MI:0914”(association)	0.530
SCRN2	TINF2	psi-mi:“MI:0915”(physical association)	0.510
SCRN2	TERF2IP	psi-mi:“MI:0915”(physical association)	0.370
SCRN2	CCS	psi-mi:“MI:0914”(association)	0.350
PDPK1	HSPA8	psi-mi:“MI:0914”(association)	0.350
SCRN2	IFI30	psi-mi:“MI:0914”(association)	0.350
TINF2	SCRN2	psi-mi:“MI:0915”(physical association)	0.000
SCRN2	PEX5	psi-mi:“MI:0915”(physical association)	0.000
SCRN2	MEOX2	psi-mi:“MI:0915”(physical association)	0.000
KAT5	SCRN2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (40): SCRN2 (Affinity Capture-MS), SCRN2 (Affinity Capture-MS), CAMK2D (Affinity Capture-MS), CCS (Affinity Capture-MS), XRN1 (Affinity Capture-MS), FAM122B (Affinity Capture-MS), DCAF10 (Affinity Capture-MS), PRRC2B (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), SCRN2 (Co-fractionation), CCS (Affinity Capture-MS), FAM122B (Affinity Capture-MS), XRN1 (Affinity Capture-MS), SCRN2 (Affinity Capture-MS), SCRN2 (Affinity Capture-MS)

ESM2 similar proteins: A4FV98, A5D7B1, A5PK51, A6QLN9, A8MUP2, D3ZVU9, O15527, O35595, O75078, O95848, P57775, Q05B60, Q06643, Q14728, Q14CX5, Q1LZB9, Q27HK4, Q2T9T5, Q2TBS1, Q3UGX3, Q4R3I0, Q4V892, Q58CT4, Q5E9H2, Q5RCI5, Q5SUV1, Q5TM22, Q642A6, Q6IA17, Q6PCB0, Q6XQN6, Q862Z7, Q8N8L6, Q8R2R5, Q8R2Z5, Q8R366, Q8WUG5, Q95JH0, Q95JH2, Q969P0

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1234 predictions. Top by Δscore:

Variant	Effect	Δscore
17:47838446:CAGAC:C	acceptor_gain	1.0000
17:47838448:GACC:G	acceptor_loss	1.0000
17:47838451:CTAG:C	acceptor_loss	1.0000
17:47838452:T:G	acceptor_loss	1.0000
17:47838692:GCCCC:G	acceptor_gain	1.0000
17:47838693:CCCC:C	acceptor_gain	1.0000
17:47838693:CCCCC:C	acceptor_gain	1.0000
17:47838694:CCC:C	acceptor_gain	1.0000
17:47838694:CCCC:C	acceptor_gain	1.0000
17:47838695:CC:C	acceptor_gain	1.0000
17:47838695:CCC:C	acceptor_gain	1.0000
17:47838696:CC:C	acceptor_gain	1.0000
17:47838696:CCT:C	acceptor_loss	1.0000
17:47838697:C:A	acceptor_loss	1.0000
17:47838697:C:CC	acceptor_gain	1.0000
17:47838701:C:CT	acceptor_gain	1.0000
17:47838701:C:T	acceptor_gain	1.0000
17:47838702:A:T	acceptor_gain	1.0000
17:47838787:TAA:T	donor_loss	1.0000
17:47838788:AACC:A	donor_loss	1.0000
17:47838789:A:AC	donor_gain	1.0000
17:47838790:C:CC	donor_gain	1.0000
17:47838790:CCTTG:C	donor_gain	1.0000
17:47839002:CCCCT:C	acceptor_gain	1.0000
17:47839003:CCCT:C	acceptor_gain	1.0000
17:47839003:CCCTC:C	acceptor_gain	1.0000
17:47839004:CCTC:C	acceptor_gain	1.0000
17:47839005:CT:C	acceptor_gain	1.0000
17:47839006:TCTG:T	acceptor_loss	1.0000
17:47839007:C:CC	acceptor_gain	1.0000

AlphaMissense

2761 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:47838605:G:C	S288R	0.990
17:47838605:G:T	S288R	0.990
17:47838607:T:G	S288R	0.990
17:47840748:G:C	N32K	0.988
17:47840748:G:T	N32K	0.988
17:47838441:G:C	F316L	0.987
17:47838441:G:T	F316L	0.987
17:47838443:A:G	F316L	0.987
17:47838438:T:A	K317N	0.985
17:47838438:T:G	K317N	0.985
17:47840319:G:C	S76R	0.984
17:47840319:G:T	S76R	0.984
17:47840321:T:G	S76R	0.984
17:47840797:A:T	V16D	0.977
17:47840201:C:G	D116H	0.975
17:47839629:C:G	R124P	0.972
17:47840751:C:A	K31N	0.972
17:47840751:C:G	K31N	0.972
17:47840280:G:C	N89K	0.971
17:47840280:G:T	N89K	0.971
17:47840285:C:G	A88P	0.971
17:47838442:A:G	F316S	0.969
17:47839643:C:A	R119S	0.969
17:47839643:C:G	R119S	0.969
17:47840300:C:A	G83W	0.968
17:47839517:G:C	F161L	0.967
17:47839517:G:T	F161L	0.967
17:47839519:A:G	F161L	0.967
17:47840300:C:G	G83R	0.966
17:47840300:C:T	G83R	0.966

dbSNP variants (sampled 300 via entrez): RS1000443986 (17:47841219 C>G,T), RS1000475114 (17:47841013 A>C), RS1000612511 (17:47840939 C>G,T), RS1000643593 (17:47840586 C>G,T), RS1001163366 (17:47842728 T>A), RS1002220000 (17:47842228 T>C), RS1002934004 (17:47839093 A>G), RS1003146794 (17:47837474 T>C), RS1004272188 (17:47841343 T>C), RS1004449794 (17:47839529 G>A,C), RS1004707786 (17:47841801 A>C), RS1004754476 (17:47841239 C>T), RS1004770 (17:47839781 C>A,G,T), RS1005449950 (17:47838156 T>C), RS1005655 (17:47842099 C>G,T)

Disease associations

OMIM: gene MIM:614966 | 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
GCST008916_117	Asthma	1.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation, affects cotreatment, increases expression	5
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	4
Arsenic	decreases expression, increases abundance, affects methylation, affects cotreatment	3
bisphenol A	decreases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
bisphenol F	increases expression	1
methylmercuric chloride	decreases expression	1
beta-lapachone	decreases expression	1
tetrabromobisphenol A	decreases expression	1
perfluorooctanoic acid	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
K 7174	decreases expression	1
bisphenol B	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	decreases expression	1
bisphenol AF	increases expression	1
Vehicle Emissions	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Curcumin	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1

Clinical trials (associated diseases)

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