SNED1

Summary

SNED1 (sushi, nidogen and EGF like domains 1, HGNC:24696) is a protein-coding gene on chromosome 2q37.3, encoding Sushi, nidogen and EGF-like domain-containing protein 1 (Q8TER0).

Predicted to enable Notch binding activity. Predicted to be involved in cell-matrix adhesion. Located in extracellular matrix.

Source: NCBI Gene 25992 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_001080437

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24696
Approved symbol	SNED1
Name	sushi, nidogen and EGF like domains 1
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ00133, SST3, Snep
Ensembl gene	ENSG00000162804
Ensembl biotype	protein_coding
OMIM	616634
Entrez	25992

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 12 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000310397, ENST00000401644, ENST00000401884, ENST00000405547, ENST00000420591, ENST00000431690, ENST00000466618, ENST00000469006, ENST00000483962, ENST00000491761, ENST00000493358, ENST00000858292, ENST00000929493, ENST00000957409, ENST00000957410, ENST00000957411, ENST00000957412

RefSeq mRNA: 1 — MANE Select: NM_001080437 NM_001080437

CCDS: CCDS46562

Canonical transcript exons

ENST00000310397 — 32 exons

Exon	Start	End
ENSE00001068753	241040300	241040413
ENSE00001068761	241048315	241048440
ENSE00001068763	241062791	241062904
ENSE00001068766	241052041	241052157
ENSE00001205633	241073266	241073364
ENSE00001205642	241063587	241063700
ENSE00001205697	241034568	241034730
ENSE00001205703	241033735	241033875
ENSE00001205751	241030284	241030571
ENSE00001844216	241091638	241095568
ENSE00003470611	241037240	241037353
ENSE00003485972	241067764	241067947
ENSE00003491871	241071796	241071878
ENSE00003510676	241040075	241040188
ENSE00003517333	241065299	241065595
ENSE00003529196	241064844	241064957
ENSE00003533195	241068911	241069023
ENSE00003541292	241069920	241070201
ENSE00003555876	241051744	241051860
ENSE00003575473	241036790	241036915
ENSE00003591067	241053153	241053326
ENSE00003593387	241049022	241049135
ENSE00003603912	241082277	241082364
ENSE00003607624	241048662	241048766
ENSE00003632247	241087392	241087475
ENSE00003638259	241071576	241071720
ENSE00003642390	241064012	241064125
ENSE00003658013	241052355	241052468
ENSE00003661046	241049817	241049933
ENSE00003670981	241081677	241081793
ENSE00003688435	241088365	241088402
ENSE00003849464	240998618	240999050

Expression profiles

Bgee: expression breadth ubiquitous, 228 present calls, max score 94.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.4583 / max 296.1264, expressed in 1262 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26481	3.7065	1098
26480	3.6764	662
26488	0.3541	98
26482	0.2651	145
26479	0.1734	82
26486	0.0969	53
26483	0.0789	27
26487	0.0602	40
26489	0.0257	13
26490	0.0212	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	94.54	gold quality
tendon of biceps brachii	UBERON:0008188	94.23	gold quality
layer of synovial tissue	UBERON:0007616	92.97	gold quality
endocervix	UBERON:0000458	92.91	gold quality
right lobe of thyroid gland	UBERON:0001119	92.35	gold quality
descending thoracic aorta	UBERON:0002345	91.93	gold quality
left lobe of thyroid gland	UBERON:0001120	91.82	gold quality
thyroid gland	UBERON:0002046	91.49	gold quality
synovial joint	UBERON:0002217	91.36	gold quality
thoracic aorta	UBERON:0001515	91.04	gold quality
ascending aorta	UBERON:0001496	91.01	gold quality
tibia	UBERON:0000979	89.95	gold quality
diaphragm	UBERON:0001103	89.86	gold quality
tibial nerve	UBERON:0001323	89.37	gold quality
mucosa of stomach	UBERON:0001199	89.25	gold quality
skin of hip	UBERON:0001554	89.13	gold quality
left ovary	UBERON:0002119	89.13	gold quality
right ovary	UBERON:0002118	89.06	gold quality
gluteal muscle	UBERON:0002000	88.98	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.75	gold quality
omental fat pad	UBERON:0010414	88.18	gold quality
peritoneum	UBERON:0002358	88.15	gold quality
body of uterus	UBERON:0009853	88.06	gold quality
left uterine tube	UBERON:0001303	88.05	gold quality
adipose tissue of abdominal region	UBERON:0007808	87.97	gold quality
gastrocnemius	UBERON:0001388	87.79	gold quality
gall bladder	UBERON:0002110	87.47	gold quality
triceps brachii	UBERON:0001509	87.21	gold quality
right coronary artery	UBERON:0001625	87.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.98	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-2	yes	2517.11
E-CURD-119	yes	34.55
E-ANND-3	yes	14.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting SNED1, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-5589-3P	99.29	68.30	1443

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	sned1	ENSDARG00000044433
mus_musculus	Sned1	ENSMUSG00000047793
rattus_norvegicus	Sned1	ENSRNOG00000023548

Paralogs (7): NOTCH3 (ENSG00000074181), NOTCH2 (ENSG00000134250), NOTCH1 (ENSG00000148400), NOTCH2NLA (ENSG00000264343), NOTCH2NLB (ENSG00000286019), NOTCH2NLR (ENSG00000286106), NOTCH2NLC (ENSG00000286219)

Protein

Protein identifiers

Sushi, nidogen and EGF-like domain-containing protein 1 — Q8TER0 (reviewed: Q8TER0)

Alternative names: Insulin-responsive sequence DNA-binding protein 1

All UniProt accessions (4): Q8TER0, H7BYY9, H7C0D4, H7C1R9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Post-translational modifications. Phosphorylated on serine and threonine residues. N-glycosylated.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8TER0-1	1	yes
Q8TER0-3	2
Q8TER0-4	3
Q8TER0-5	4

RefSeq proteins (1): NP_001073906* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000152	EGF-type_Asp/Asn_hydroxyl_site	PTM
IPR000436	Sushi_SCR_CCP_dom	Domain
IPR000742	EGF	Domain
IPR001881	EGF-like_Ca-bd_dom	Domain
IPR003886	NIDO_dom	Domain
IPR003961	FN3_dom	Domain
IPR013032	EGF-like_CS	Conserved_site
IPR013783	Ig-like_fold	Homologous_superfamily
IPR018097	EGF_Ca-bd_CS	Conserved_site
IPR035976	Sushi/SCR/CCP_sf	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR051830	NOTCH_homolog	Family

Pfam: PF00008, PF00041, PF06119, PF12661

UniProt features (103 total): disulfide bond 47, domain 22, glycosylation site 14, splice variant 6, sequence conflict 5, sequence variant 4, region of interest 2, signal peptide 1, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TER0-F1	71.94	0.17

Functional residue map

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

Disulfide bonds (47): 272–284, 278–297, 299–308, 315–326, 320–335, 337–346, 353–364, 358–373, 375–384, 391–402, 396–411, 413–422, 433–444, 438–453, 455–464, 472–480, 474–488, 490–499, 545–556, 550–565 …

Glycosylation sites (14): 145, 204, 292, 368, 408, 484, 536, 712, 886, 977, 1015, 1109, 1139, 1310

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): BROWNE_HCMV_INFECTION_48HR_DN, CAIRO_HEPATOBLASTOMA_CLASSES_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, MODULE_480, ONDER_CDH1_TARGETS_2_UP, BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP, GOMF_SIGNALING_RECEPTOR_BINDING, GOBP_CELL_SUBSTRATE_ADHESION, GOBP_CELL_MATRIX_ADHESION, MILI_PSEUDOPODIA_CHEMOTAXIS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, MODULE_427, VALK_AML_CLUSTER_10, GOMF_NOTCH_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN

GO Biological Process (1): cell-matrix adhesion (GO:0007160)

GO Molecular Function (3): Notch binding (GO:0005112), calcium ion binding (GO:0005509), protein binding (GO:0005515)

GO Cellular Component (3): extracellular matrix (GO:0031012), extracellular region (GO:0005576), plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell-substrate adhesion	1
signaling receptor binding	1
metal ion binding	1
binding	1
external encapsulating structure	1
cellular anatomical structure	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1403 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNED1	SST	P01166	825
SNED1	CORT	O00230	579
SNED1	SSTR2	P30874	507
SNED1	SUSD5	O60279	426
SNED1	SSTR1	P30872	417
SNED1	MMEL1	Q495T6	410
SNED1	MME	P08473	405
SNED1	NAT10	Q9H0A0	382
SNED1	QPRT	Q15274	378
SNED1	CCDC80	Q76M96	375
SNED1	GH1	P01241	365
SNED1	ASGR2	P07307	363
SNED1	FAU	P35544	352
SNED1	SSTR3	P32745	348
SNED1	RELN	P78509	346

IntAct

3 interactions, top by confidence:

A	B	Type	Score
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
ESR2	PSMD11	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): SNED1 (Affinity Capture-MS), SNED1 (Affinity Capture-MS), SNED1 (Affinity Capture-MS), SNED1 (Protein-RNA), SNED1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A096LNW5, B8JI71, D3ZHH1, G3I6Z6, O00548, O35516, O57409, P0DPK3, P0DPK4, P35442, P46531, P78504, P97677, Q01705, Q04721, Q05793, Q07008, Q08E66, Q2QI47, Q5G872, Q5ZQU0, Q61483, Q63722, Q66PY1, Q6DI48, Q6NZL8, Q70E20, Q7TQN3, Q7Z3S9, Q8IWY4, Q8IX30, Q8JZM4, Q8K3K1, Q8NFT8, Q8TER0, Q8TEU8, Q8UWJ4, Q8VHS2, Q90Y54, Q90Y57

Diamond homologs: A0A1F4, D3ZHH1, G5EDK5, O35474, O43854, O88277, P10040, P13508, P14585, P18168, P78504, P97607, Q06561, Q19319, Q20911, Q501P1, Q53RD9, Q5R7K9, Q5ZQU0, Q63722, Q6R8J2, Q70E20, Q8TER0, Q90Y54, Q90Y57, Q9JLB4, Q9QXX0, Q9QYE5, Q9W332, Q9Y219, A0A6G9KJM3, A0A8U0LTM5, A0A8U0LTN3, A0A8U0LTT7, A0A8U0LTT9, A0A8U0LU66, D3ZUK3, O93383, P01132, P07522

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	4
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

7958 predictions. Top by Δscore:

Variant	Effect	Δscore
2:240999048:TAC:T	donor_gain	1.0000
2:240999049:AC:A	donor_gain	1.0000
2:240999049:ACG:A	donor_loss	1.0000
2:240999050:CGTG:C	donor_loss	1.0000
2:240999051:G:GG	donor_gain	1.0000
2:241030555:G:GT	donor_gain	1.0000
2:241030572:G:GG	donor_gain	1.0000
2:241033871:CCCAG:C	donor_loss	1.0000
2:241033874:AGGTA:A	donor_loss	1.0000
2:241033875:GG:G	donor_loss	1.0000
2:241033876:GTAG:G	donor_loss	1.0000
2:241033877:T:A	donor_loss	1.0000
2:241034566:AGGCT:A	acceptor_gain	1.0000
2:241034567:GGCTG:G	acceptor_gain	1.0000
2:241036789:GC:G	acceptor_gain	1.0000
2:241036914:GG:G	donor_gain	1.0000
2:241036915:GG:G	donor_gain	1.0000
2:241036916:GT:G	donor_loss	1.0000
2:241048389:GGC:G	donor_gain	1.0000
2:241048436:G:GT	donor_gain	1.0000
2:241048441:G:GG	donor_gain	1.0000
2:241052036:TCCA:T	acceptor_loss	1.0000
2:241052037:CCA:C	acceptor_loss	1.0000
2:241052038:CA:C	acceptor_loss	1.0000
2:241052039:A:AC	acceptor_loss	1.0000
2:241052039:A:AG	acceptor_gain	1.0000
2:241052039:AG:A	acceptor_gain	1.0000
2:241052040:G:GG	acceptor_gain	1.0000
2:241052040:GG:G	acceptor_gain	1.0000
2:241052154:A:G	donor_gain	1.0000

AlphaMissense

9250 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:241065363:G:C	W926C	0.998
2:241065363:G:T	W926C	0.998
2:241065565:A:C	S994R	0.997
2:241065567:C:A	S994R	0.997
2:241065567:C:G	S994R	0.997
2:241052088:T:C	C634R	0.996
2:241052090:C:G	C634W	0.996
2:241052115:T:A	C643S	0.996
2:241052116:G:C	C643S	0.996
2:241065361:T:A	W926R	0.996
2:241065361:T:C	W926R	0.996
2:241065413:T:A	V943D	0.996
2:241069982:T:A	W1124R	0.996
2:241069982:T:C	W1124R	0.996
2:241069984:G:C	W1124C	0.996
2:241069984:G:T	W1124C	0.996
2:241030296:G:T	G76W	0.995
2:241030383:T:A	W105R	0.995
2:241030383:T:C	W105R	0.995
2:241030385:G:C	W105C	0.995
2:241030385:G:T	W105C	0.995
2:241036834:T:A	C284S	0.995
2:241036835:G:C	C284S	0.995
2:241049924:T:A	C576S	0.995
2:241049925:G:C	C576S	0.995
2:241051836:T:C	F610L	0.995
2:241051838:C:A	F610L	0.995
2:241051838:C:G	F610L	0.995
2:241051851:T:A	C615S	0.995
2:241051852:G:A	C615Y	0.995

dbSNP variants (sampled 300 via entrez): RS1000015077 (2:241076422 G>T), RS1000028502 (2:241033281 G>C,T), RS1000081873 (2:241032936 A>T), RS1000107414 (2:241090887 A>G), RS1000165938 (2:240999539 G>C), RS1000183184 (2:241001113 G>A,C), RS1000184078 (2:241037535 G>A), RS1000196783 (2:241075563 C>A), RS1000210579 (2:241061884 A>G), RS1000217825 (2:241045038 G>A), RS1000235587 (2:241001389 A>G), RS1000242987 (2:241081677 A>G,T), RS1000316041 (2:241032683 T>C), RS1000340659 (2:241087751 G>A), RS1000352817 (2:241070666 G>A)

Disease associations

OMIM: gene MIM:616634 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001554_3	Sex hormone-binding globulin levels	3.000000e-06
GCST002888_1	Pharmacokinetics of antipsychotic drugs in severe mental disorder (concentration drug ratio)	4.000000e-07
GCST003998_4	Joint mobility (Beighton score)	6.000000e-12
GCST008839_576	Height	1.000000e-11
GCST012227_981	Hip circumference adjusted for BMI	8.000000e-11
GCST90020028_711	Hip circumference adjusted for BMI	4.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004696	sex hormone-binding globulin measurement
EFO:0007635	concentration dose ratio
EFO:0007905	joint hypermobility measurement
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

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	3
Tobacco Smoke Pollution	decreases expression, decreases methylation	2
bisphenol A	decreases methylation	1
nickel sulfate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Doxorubicin	affects expression	1
Thiram	decreases expression	1
Valproic Acid	increases methylation	1
Isotretinoin	increases expression	1
Aflatoxin B1	decreases expression, increases methylation	1
Antirheumatic Agents	decreases expression	1
S-Nitrosoglutathione	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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