SORCS2

Summary

SORCS2 (sortilin related VPS10 domain containing receptor 2, HGNC:16698) is a protein-coding gene on chromosome 4p16.1, encoding VPS10 domain-containing receptor SorCS2 (Q96PQ0). The heterodimer formed by NGFR and SORCS2 functions as receptor for the precursor forms of NGF (proNGF) and BDNF (proBDNF).

This gene encodes one family member of vacuolar protein sorting 10 (VPS10) domain-containing receptor proteins. The VPS10 domain name comes from the yeast carboxypeptidase Y sorting receptor Vps10 protein. Members of this gene family are large with many exons but the CDS lengths are usually less than 3700 nt. Very large introns typically separate the exons encoding the VPS10 domain; the remaining exons are separated by much smaller-sized introns. These genes are strongly expressed in the central nervous system.

Source: NCBI Gene 57537 — RefSeq curated summary.

At a glance

• GWAS associations: 23
• Clinical variants (ClinVar): 276 total
• MANE Select transcript: NM_020777

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16698
Approved symbol	SORCS2
Name	sortilin related VPS10 domain containing receptor 2
Location	4p16.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1329
Ensembl gene	ENSG00000184985
Ensembl biotype	protein_coding
OMIM	606284
Entrez	57537

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000505529, ENST00000507866, ENST00000511199

RefSeq mRNA: 1 — MANE Select: NM_020777 NM_020777

CCDS: CCDS47008

Canonical transcript exons

ENST00000507866 — 27 exons

Exon	Start	End
ENSE00001290696	7697198	7697274
ENSE00001291529	7676050	7676229
ENSE00001292853	7726780	7726903
ENSE00001293695	7723697	7723883
ENSE00001297286	7664353	7664471
ENSE00001299858	7728350	7728462
ENSE00001303565	7733322	7733421
ENSE00001305708	7715183	7715311
ENSE00001306165	7712733	7712853
ENSE00001312218	7737069	7737172
ENSE00001312549	7682743	7682889
ENSE00001312811	7667124	7667213
ENSE00001313408	7725154	7725287
ENSE00001314492	7718012	7718183
ENSE00001314504	7704177	7704284
ENSE00001315134	7689486	7689588
ENSE00001319221	7703280	7703371
ENSE00001319586	7661500	7661564
ENSE00001320586	7734272	7734374
ENSE00001322440	7729587	7729712
ENSE00001329054	7714240	7714373
ENSE00001554546	7192538	7193126
ENSE00002050013	7740200	7742827
ENSE00003497867	7396288	7396355
ENSE00003502301	7654134	7654207
ENSE00003581784	7638328	7638492
ENSE00003623859	7531530	7531629

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 87.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0274 / max 129.8001, expressed in 951 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
46829	6.0274	951

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	87.88	gold quality
tibial nerve	UBERON:0001323	85.24	gold quality
sural nerve	UBERON:0015488	84.52	gold quality
nucleus accumbens	UBERON:0001882	84.26	gold quality
caudate nucleus	UBERON:0001873	83.96	gold quality
putamen	UBERON:0001874	83.60	gold quality
Brodmann (1909) area 23	UBERON:0013554	82.17	gold quality
right frontal lobe	UBERON:0002810	82.04	gold quality
primary visual cortex	UBERON:0002436	81.88	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.48	gold quality
anterior cingulate cortex	UBERON:0009835	81.42	gold quality
amygdala	UBERON:0001876	81.25	gold quality
middle temporal gyrus	UBERON:0002771	81.03	silver quality
prefrontal cortex	UBERON:0000451	80.97	gold quality
neocortex	UBERON:0001950	80.44	gold quality
frontal cortex	UBERON:0001870	80.30	gold quality
occipital lobe	UBERON:0002021	80.18	gold quality
temporal lobe	UBERON:0001871	80.05	gold quality
medial globus pallidus	UBERON:0002477	79.88	gold quality
inferior vagus X ganglion	UBERON:0005363	79.78	silver quality
cerebral cortex	UBERON:0000956	79.49	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	79.25	gold quality
ventricular zone	UBERON:0003053	78.97	gold quality
tibia	UBERON:0000979	78.89	silver quality
forebrain	UBERON:0001890	78.88	gold quality
globus pallidus	UBERON:0001875	78.81	gold quality
tendon of biceps brachii	UBERON:0008188	78.78	gold quality
Ammon’s horn	UBERON:0001954	78.45	gold quality
entorhinal cortex	UBERON:0002728	78.26	gold quality
endocervix	UBERON:0000458	78.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

149 targeting SORCS2, 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-6748-5P	100.00	65.81	1057
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085

Literature-anchored findings (GeneRIF, showing 8)

• Sortilin-related receptor CNS expressed 2 (SorCS2) is one of the vacuolar protein sorting 10 family proteins which may be involved in the disease process of amyotrophic lateral sclerosis (PMID:26420026)
• Here the authors have characterized SorCS1, SorCS2 and SorCS3 using biochemical methods and electron microscopy. They found that their purified extracellular domains co-exist in stable dimeric and monomeric populations. (PMID:28827148)
• The rs73208473, within intron 1 of SORCS2 is associated with atazanavir exposure measured in hair. (PMID:29315502)
• We used human neural lineage cells to demonstrate in vitro a causal relationship between stress hormone levels and SORCS2 expression, and show that SORCS2 levels in culture are increased upon ethanol exposure and withdrawal (PMID:30252935)
• Findings highlight a protective role for SorCS2 in neuronal stress response and provide a possible explanation for upregulation of this receptor seen in surviving neurons of the human epileptic brain. (PMID:30840898)
• Association of Pharmacogenetic Markers With Atazanavir Exposure in HIV-Infected Women. (PMID:31562781)
• Loss of SORCS2 is Associated with Neuronal DNA Double-Strand Breaks. (PMID:34741697)
• Alternative splicing regulates adaptor protein binding, trafficking, and activity of the Vps10p domain receptor SorCS2 in neuronal development. (PMID:37507021)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	sorcs2	ENSDARG00000077465
mus_musculus	Sorcs2	ENSMUSG00000029093
rattus_norvegicus	Sorcs2	ENSRNOG00000007033

Paralogs (4): SORCS1 (ENSG00000108018), SORT1 (ENSG00000134243), SORL1 (ENSG00000137642), SORCS3 (ENSG00000156395)

Protein

Protein identifiers

VPS10 domain-containing receptor SorCS2 — Q96PQ0 (reviewed: Q96PQ0)

All UniProt accessions (2): Q96PQ0, H0Y9I2

UniProt curated annotations — full annotation on UniProt →

Function. The heterodimer formed by NGFR and SORCS2 functions as receptor for the precursor forms of NGF (proNGF) and BDNF (proBDNF). ProNGF and proBDNF binding both promote axon growth cone collapse (in vitro). Plays a role in the regulation of dendritic spine density in hippocampus neurons. Required for normal neurite branching and extension in response to BDNF. Plays a role in BDNF-dependent hippocampal synaptic plasticity. Together with NGFR and NTRK2, is required both for BDNF-mediated synaptic long-term depression and long-term potentiation. ProNGF binding promotes dissociation of TRIO from the heterodimer, which leads to inactivation of RAC1 and/or RAC2 and subsequent reorganization of the actin cytoskeleton. Together with the retromer complex subunit VPS35, required for normal expression of GRIN2A at synapses and dendritic cell membranes. Required for normal expression of the amino acid transporter SLC1A1 at the cell membrane, and thereby contributes to protect cells against oxidative stress. Does not promote Schwann cell apoptosis in response to proBDNF. SorCS2 104 kDa chain and SorCS2 18 kDa chain together promote Schwann cell apoptosis in response to proBDNF.

Subunit / interactions. Homodimer (in vitro). Heterodimer with NGFR. The extracellular domains of the heterodimer bind the precursor form of NGF (proNGF). Has much higher affinity for proNGF than for mature NGF. Can also bind mature NGF and BDNF. Each chain in the receptor dimer interacts (via extracellular domain) with an NGF dimer (in vitro). Interacts with the precursor forms of BDNF (proBDNF) and NTF3 (proNT3). The cytoplasmic region of the heterodimer formed by NGFR and SORCS2 binds TRIO. ProNGF binding mediates dissociation of TRIO from the receptor complex. Interacts with SLC1A1. Interacts with VPS35. Interacts (via extracellular domain) with NTRK2 (via extracellular domain). Interacts with VPS35. Interacts (via extracellular domain) with GRIN2A.

Subcellular location. Cell membrane. Cell projection. Cytoplasmic vesicle membrane. Early endosome membrane. Recycling endosome membrane. Synapse. Synaptosome. Perikaryon. Dendrite. Dendritic spine. Postsynaptic density membrane.

Tissue specificity. Detected on neurons in the caudate region. Detected on neurons in the hippocampus (at protein level). Highly expressed in brain and kidney. Detected at low levels in heart, liver, small intestine, skeletal muscle and thymus.

Post-translational modifications. Proteolytic cleavage removes a propeptide, giving rise to a 122 kDa chain that includes a cytoplasmic tail. Further cleavage gives rise to a 104 kDa chain that lacks the cytoplasmic tail, and a membrane-bound 18 kDa chain. The 104 kDa chain remains bound to the 18 kDa chain. N-glycosylated.

Miscellaneous. Expression is decreased in the brains of Huntington disease (HD) patients after the onset of symptoms.

Similarity. Belongs to the VPS10-related sortilin family. SORCS subfamily.

RefSeq proteins (1): NP_065828* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000601	PKD_dom	Domain
IPR006581	VPS10	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR022409	PKD/Chitinase_dom	Domain
IPR031777	Sortilin_C	Domain
IPR031778	Sortilin_N	Domain
IPR035986	PKD_dom_sf	Homologous_superfamily
IPR050310	VPS10-sortilin	Family

Pfam: PF00801, PF15901, PF15902

UniProt features (57 total): strand 8, glycosylation site 7, disulfide bond 7, repeat 6, region of interest 5, chain 4, mutagenesis site 4, site 3, sequence variant 3, domain 2, compositionally biased region 2, topological domain 2, signal peptide 1, sequence conflict 1, helix 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
1WGO	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96PQ0-F1	78.82	0.45

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 (3): 69–70 (cleavage); 119–120 (cleavage); 1030–1031 (cleavage)

Disulfide bonds (7): 324–329, 494–499, 649–684, 667–699, 701–760, 708–725, 740–775

Glycosylation sites (7): 158, 328, 362, 600, 830, 891, 902

Mutagenesis-validated functional residues (4):

Position	Phenotype
66–69	decreased proteolytic processing; when associated with 116-a–a-119.
116–119	decreased proteolytic processing; when associated with 66-a–a-69.
1027	strongly increases generation of the 104 kda chain.
1028–1030	abolishes generation of the 104 kda chain.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP, ACTGCAG_MIR173P, GOBP_CELL_CELL_SIGNALING, CCANNAGRKGGC_UNKNOWN, GOBP_REGULATION_OF_SYNAPTIC_PLASTICITY, GOBP_LONG_TERM_SYNAPTIC_DEPRESSION, MYOD_01, GOBP_NEGATIVE_REGULATION_OF_SYNAPTIC_TRANSMISSION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, chr4p16, GOZGIT_ESR1_TARGETS_UP, GOBP_SYNAPTIC_SIGNALING, GOMF_PEPTIDE_RECEPTOR_ACTIVITY, GOCC_NEURON_PROJECTION

GO Biological Process (3): intracellular protein transport (GO:0006886), neuropeptide signaling pathway (GO:0007218), long-term synaptic depression (GO:0060292)

GO Molecular Function (2): neuropeptide receptor activity (GO:0008188), protein binding (GO:0005515)

GO Cellular Component (18): cytosol (GO:0005829), membrane (GO:0016020), early endosome membrane (GO:0031901), dendritic spine (GO:0043197), perikaryon (GO:0043204), recycling endosome membrane (GO:0055038), postsynaptic density membrane (GO:0098839), cytoplasm (GO:0005737), endosome (GO:0005768), plasma membrane (GO:0005886), postsynaptic density (GO:0014069), dendrite (GO:0030425), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410), cell projection (GO:0042995), neuron projection (GO:0043005), synapse (GO:0045202), postsynaptic membrane (GO:0045211)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cytoplasm	2
endosome membrane	2
postsynapse	2
cytoplasmic vesicle	2
intracellular protein localization	1
protein transport	1
intracellular transport	1
G protein-coupled receptor signaling pathway	1
regulation of synaptic plasticity	1
negative regulation of synaptic transmission	1
neuropeptide signaling pathway	1
G protein-coupled peptide receptor activity	1
neuropeptide binding	1
binding	1
early endosome	1
dendrite	1
neuron spine	1
neuronal cell body	1
recycling endosome	1
postsynaptic density	1
postsynaptic membrane	1
postsynaptic specialization membrane	1
intracellular anatomical structure	1
endomembrane system	1
membrane	1
cell periphery	1
asymmetric synapse	1
postsynaptic specialization	1
neuron projection	1
dendritic tree	1
vesicle membrane	1
intracellular vesicle	1
plasma membrane bounded cell projection	1
cell junction	1
synaptic membrane	1

Protein interactions and networks

STRING

1128 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SORCS2	NGFR	P08138	894
SORCS2	BDNF	P23560	820
SORCS2	SORT1	Q99523	729
SORCS2	VPS35	Q96QK1	671
SORCS2	PSRC1	Q6PGN9	670
SORCS2	CELSR2	Q9HCU4	662
SORCS2	NGF	P01138	509
SORCS2	RABIF	P47224	462
SORCS2	SH3TC1	Q8TE82	458
SORCS2	CST3	P01034	442
SORCS2	ERC2	O15083	438
SORCS2	VPS26A	O75436	430
SORCS2	SORL1	Q92673	421
SORCS2	ABLIM2	Q6H8Q1	421
SORCS2	SNX3	O60493	420

IntAct

15 interactions, top by confidence:

A	B	Type	Score
SORCS2	Ngf	psi-mi:“MI:0407”(direct interaction)	0.440
SORCS2	NGF	psi-mi:“MI:0407”(direct interaction)	0.440
SORCS2	BDNF	psi-mi:“MI:0407”(direct interaction)	0.440
SORCS2	NTF3	psi-mi:“MI:0407”(direct interaction)	0.440
SORCS2	NGFR	psi-mi:“MI:0407”(direct interaction)	0.440
HNRNPU	SORCS2	psi-mi:“MI:0915”(physical association)	0.400
SORCS2	Ngfr	psi-mi:“MI:0915”(physical association)	0.400
ITM2B	ILVBL	psi-mi:“MI:0914”(association)	0.350
MYH4	PALM3	psi-mi:“MI:0914”(association)	0.350
SORCS2	HMGCR	psi-mi:“MI:0914”(association)	0.350
SYT2	SMAP	psi-mi:“MI:0914”(association)	0.350
TMEM169	PTGES3L-AARSD1	psi-mi:“MI:0914”(association)	0.350
ATF3	TMEM223	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): SORCS2 (Affinity Capture-RNA), SORCS2 (Proximity Label-MS), SORCS2 (Affinity Capture-MS), NXT2 (Affinity Capture-MS), HMGCR (Affinity Capture-MS), SORCS2 (Affinity Capture-MS), TTC1 (Affinity Capture-MS), DCAF10 (Affinity Capture-MS), CSTF2T (Affinity Capture-MS), FNDC3A (Affinity Capture-MS), SORCS2 (Affinity Capture-MS), SORCS2 (Co-fractionation), SORCS2 (Co-fractionation), SORCS2 (Affinity Capture-RNA)

ESM2 similar proteins: A0A1B0GTW7, A0A1D5NSK0, A0A1L8HYT7, A0A286YEC0, G7PWZ3, O77755, O88959, P0C0K7, P17490, P23276, P43021, P51882, P59509, P59996, P70505, Q02853, Q04912, Q04962, Q04997, Q0V8J4, Q0VAY3, Q17R55, Q3U435, Q499S5, Q4R7Z5, Q58Y75, Q62190, Q6MG64, Q76MJ5, Q7TN88, Q7Z442, Q80W65, Q8BMN4, Q8CJH3, Q8IVN8, Q8VCS0, Q91X21, Q96KR4, Q96PQ0, Q96S42

Diamond homologs: Q8VI51, Q8WY21, Q96PQ0, Q9EPR5, Q9JLC4, Q9UPU3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	221
Likely benign	11
Benign	11

Top pathogenic / likely-pathogenic (0)

SpliceAI

9969 predictions. Top by Δscore:

Variant	Effect	Δscore
4:7193122:GCAGC:G	donor_gain	1.0000
4:7193125:GC:G	donor_gain	1.0000
4:7193127:G:GG	donor_gain	1.0000
4:7396281:A:AG	acceptor_gain	1.0000
4:7396354:CGGTA:C	donor_loss	1.0000
4:7396355:GGT:G	donor_loss	1.0000
4:7396356:GTAA:G	donor_loss	1.0000
4:7396357:T:G	donor_loss	1.0000
4:7531528:A:AG	acceptor_gain	1.0000
4:7531528:AG:A	acceptor_gain	1.0000
4:7531529:G:GA	acceptor_gain	1.0000
4:7531529:GG:G	acceptor_gain	1.0000
4:7531529:GGT:G	acceptor_gain	1.0000
4:7531529:GGTC:G	acceptor_gain	1.0000
4:7531529:GGTCA:G	acceptor_gain	1.0000
4:7531625:GGAAG:G	donor_gain	1.0000
4:7531626:G:GT	donor_gain	1.0000
4:7531626:GAAG:G	donor_gain	1.0000
4:7531627:A:T	donor_gain	1.0000
4:7531627:AAGG:A	donor_loss	1.0000
4:7531630:G:GG	donor_gain	1.0000
4:7531631:T:G	donor_loss	1.0000
4:7638324:TCA:T	acceptor_loss	1.0000
4:7638324:TCAGG:T	acceptor_gain	1.0000
4:7638325:CAGG:C	acceptor_gain	1.0000
4:7638326:A:AG	acceptor_gain	1.0000
4:7638326:AG:A	acceptor_gain	1.0000
4:7638326:AGGT:A	acceptor_loss	1.0000
4:7638326:AGGTC:A	acceptor_gain	1.0000
4:7638327:G:GG	acceptor_gain	1.0000

AlphaMissense

7522 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:7396301:T:C	L165P	1.000
4:7396355:G:C	R183P	1.000
4:7704202:T:A	W596R	1.000
4:7704202:T:C	W596R	1.000
4:7712741:G:A	G626D	1.000
4:7712764:T:A	W634R	1.000
4:7712764:T:C	W634R	1.000
4:7712766:G:C	W634C	1.000
4:7712766:G:T	W634C	1.000
4:7193106:T:A	W154R	0.999
4:7193106:T:C	W154R	0.999
4:7193108:G:C	W154C	0.999
4:7193108:G:T	W154C	0.999
4:7396342:A:C	S179R	0.999
4:7396344:T:A	S179R	0.999
4:7396344:T:G	S179R	0.999
4:7396351:T:A	W182R	0.999
4:7396351:T:C	W182R	0.999
4:7531531:T:C	S184P	0.999
4:7531543:G:T	G188W	0.999
4:7531544:G:A	G188E	0.999
4:7531552:T:G	Y191D	0.999
4:7682832:G:C	W477C	0.999
4:7682832:G:T	W477C	0.999
4:7697198:G:A	G531D	0.999
4:7697266:T:A	W554R	0.999
4:7697266:T:C	W554R	0.999
4:7703368:T:C	L586P	0.999
4:7704181:A:C	S589R	0.999
4:7704183:T:A	S589R	0.999

dbSNP variants (sampled 300 via entrez): RS1000001444 (4:7334512 TG>T), RS1000003750 (4:7423490 C>T), RS10000132 (4:7397942 T>C,G), RS1000017277 (4:7709896 C>G), RS10000185 (4:7508031 C>T), RS1000020086 (4:7650164 C>A,G,T), RS1000020304 (4:7484570 G>A), RS1000021175 (4:7247351 T>C), RS10000236 (4:7398065 T>G), RS1000026934 (4:7517151 A>G), RS10000306 (4:7683867 C>A,T), RS1000032873 (4:7487001 C>A,T), RS1000034188 (4:7645133 G>A), RS1000037047 (4:7654701 C>A,T), RS1000041626 (4:7270677 G>A)

Disease associations

OMIM: gene MIM:606284 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

23 associations (top):

Study	Trait	p-value
GCST000937_4	Insulin-like growth factors	5.000000e-10
GCST001762_16	Obesity-related traits	3.000000e-06
GCST001762_588	Obesity-related traits	9.000000e-06
GCST002097_38	Coronary artery calcification	3.000000e-06
GCST002589_10	Hippocampal sclerosis	8.000000e-06
GCST003025_5	Attention function in attention deficit hyperactive disorder	4.000000e-07
GCST003090_6	Depressive and manic episodes in bipolar disorder	4.000000e-06
GCST003854_40	Gut microbiota (functional units)	3.000000e-09
GCST004379_1	Red blood cell density in sickle cell anemia	2.000000e-07
GCST006203_1	Atazanavir levels	2.000000e-08
GCST007059_1	Response to antidepressants (symptom improvement)	2.000000e-06
GCST007325_170	General risk tolerance (MTAG)	1.000000e-08
GCST007400_54	Systemic lupus erythematosus	4.000000e-06
GCST008137_1	Alcohol withdrawal symptoms	4.000000e-09
GCST008487_1	Coffee consumption	4.000000e-06
GCST009311_5	Letter-number span reordering	6.000000e-06
GCST010243_242	Apolipoprotein B levels	7.000000e-10
GCST010245_23	LDL cholesterol levels	3.000000e-09
GCST011155_16	Nontraumatic osteonecrosis of the femoral head	4.000000e-06
GCST011742_46	Triglyceride levels in HIV infection	8.000000e-07
GCST012136_1	Hypertension in type 2 diabetes	7.000000e-06
GCST012277_7	Clostridioides difficle infection	1.000000e-06
GCST012489_76	Heel bone mineral density x serum urate levels interaction	4.000000e-09

EFO canonical traits (18, from GWAS)

EFO ID	Trait name
EFO:0004626	IGFBP-3 measurement
EFO:0005106	body composition measurement
EFO:0004723	coronary artery calcification
EFO:0007636	attention function measurement
EFO:0007704	depressive episode measurement
EFO:0007705	manic episode measurement
EFO:0007874	gut microbiome measurement
EFO:0009306	atazanavir measurement
EFO:0008579	risk-taking behaviour
EFO:0006781	coffee consumption measurement
EFO:0004874	memory performance
EFO:0004615	apolipoprotein B measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:1001930	idiopathic osteonecrosis of the femoral head
EFO:0004530	triglyceride measurement
EFO:0009130	clostridium difficile infection
EFO:0004531	urate measurement
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs73208473	Metabolism/PK	3	atazanavir	HIV infectious disease

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs73208473	SORCS2	3	2.88	1	atazanavir

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	6
trichostatin A	affects cotreatment, decreases expression	3
Benzo(a)pyrene	affects methylation, decreases expression	3
Aflatoxin B1	affects methylation, decreases expression	3
sodium arsenite	increases expression	2
Panobinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Particulate Matter	increases abundance, increases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, affects methylation, decreases methylation	1
hydroxyhydroquinone	decreases expression	1
2,3-pentanedione	decreases expression	1
beta-lapachone	decreases expression	1
sulforaphane	decreases expression	1
benzo(e)pyrene	affects methylation, increases methylation	1
ferrous chloride	decreases expression	1
aflatoxin B2	increases methylation	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Vorinostat	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Vehicle Emissions	increases abundance, increases expression	1
Diacetyl	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	increases 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_E1M7	HyCyte MKN45 KO-hSORCS2	Cancer cell line	Female

Clinical trials (associated diseases)

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