SGIP1

Summary

SGIP1 (SH3GL interacting endocytic adaptor 1, HGNC:25412) is a protein-coding gene on chromosome 1p31.3, encoding SH3-containing GRB2-like protein 3-interacting protein 1 (Q9BQI5). May function in clathrin-mediated endocytosis.

SGIP1 functions as an endocytic protein that affects signaling by receptors in neuronal systems involved in energy homeostasis via its interaction with endophilins (see SH3GL3; MIM 603362) (Trevaskis et al., 2005 [PubMed 15919751] and Uezu et al., 2007 [PubMed 17626015]).

Source: NCBI Gene 84251 — RefSeq curated summary.

At a glance

• GWAS associations: 86
• Clinical variants (ClinVar): 141 total
• MANE Select transcript: NM_032291

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25412
Approved symbol	SGIP1
Name	SH3GL interacting endocytic adaptor 1
Location	1p31.3
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761D221
Ensembl gene	ENSG00000118473
Ensembl biotype	protein_coding
OMIM	611540
Entrez	84251

Gene structure

Transcript identifiers

Ensembl transcripts: 62 — 35 protein_coding, 13 nonsense_mediated_decay, 12 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000237247, ENST00000320161, ENST00000371037, ENST00000371039, ENST00000424320, ENST00000435165, ENST00000468286, ENST00000468570, ENST00000480548, ENST00000483060, ENST00000484988, ENST00000487507, ENST00000493564, ENST00000681971, ENST00000682032, ENST00000682054, ENST00000682150, ENST00000682270, ENST00000682293, ENST00000682416, ENST00000682419, ENST00000682476, ENST00000682519, ENST00000682619, ENST00000682707, ENST00000682762, ENST00000682816, ENST00000682894, ENST00000682901, ENST00000682938, ENST00000682981, ENST00000683067, ENST00000683207, ENST00000683257, ENST00000683291, ENST00000683311, ENST00000683499, ENST00000683526, ENST00000683581, ENST00000683604, ENST00000683731, ENST00000683911, ENST00000684083, ENST00000684168, ENST00000684178, ENST00000684369, ENST00000684539, ENST00000684563, ENST00000684651, ENST00000684664, ENST00000684750, ENST00000684751, ENST00000887101, ENST00000887102, ENST00000887103, ENST00000887104, ENST00000941748, ENST00000941749, ENST00000941750, ENST00000941751, ENST00000941752, ENST00000941753

RefSeq mRNA: 27 — MANE Select: NM_032291 NM_001308203, NM_001350217, NM_001350218, NM_001376534, NM_001376535, NM_001376536, NM_001376537, NM_001376538, NM_001376539, NM_001376540, NM_001376541, NM_001376542, NM_001376543, NM_001376544, NM_001376545, NM_001376546, NM_001376547, NM_001376548, NM_001376549, NM_001376550, NM_001376551, NM_001376552, NM_001376554, NM_001376555, NM_001376556, NM_001376557, NM_032291

CCDS: CCDS30744, CCDS76171, CCDS90969, CCDS90970, CCDS90971, CCDS90972, CCDS90973

Canonical transcript exons

ENST00000371037 — 25 exons

Exon	Start	End
ENSE00001521174	66743073	66751139
ENSE00001592228	66739335	66739537
ENSE00001612862	66667530	66667541
ENSE00001614887	66733748	66733880
ENSE00001662063	66690190	66690316
ENSE00001677601	66681869	66682369
ENSE00001702309	66741272	66741436
ENSE00001708980	66695434	66695493
ENSE00001728807	66729264	66729419
ENSE00001761898	66740658	66740722
ENSE00001773336	66660513	66660524
ENSE00001788471	66719294	66719405
ENSE00001944639	66534153	66534368
ENSE00003469818	66633070	66633094
ENSE00003487771	66635944	66636015
ENSE00003490585	66670995	66671019
ENSE00003510766	66643544	66643719
ENSE00003556405	66677004	66677096
ENSE00003561367	66673281	66673366
ENSE00003586844	66625847	66625910
ENSE00003608974	66642810	66642864
ENSE00003612796	66679678	66679752
ENSE00003626969	66689148	66689275
ENSE00003651591	66639777	66639833
ENSE00003660898	66671944	66671995

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 95.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.6211 / max 1449.7150, expressed in 966 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
3368	15.7694	920
3365	1.3699	498
3370	0.9890	272
3367	0.4638	158
201539	0.2781	116
3366	0.2552	135
201540	0.2347	116
201537	0.1586	75
201538	0.1022	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	95.92	gold quality
tibial artery	UBERON:0007610	94.11	gold quality
popliteal artery	UBERON:0002250	94.10	gold quality
descending thoracic aorta	UBERON:0002345	92.87	gold quality
aorta	UBERON:0000947	92.83	gold quality
artery	UBERON:0001637	92.36	gold quality
thoracic aorta	UBERON:0001515	91.51	gold quality
ascending aorta	UBERON:0001496	91.39	gold quality
prefrontal cortex	UBERON:0000451	91.35	gold quality
cortical plate	UBERON:0005343	91.15	gold quality
middle temporal gyrus	UBERON:0002771	91.05	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.78	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.60	gold quality
endothelial cell	CL:0000115	90.19	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.83	gold quality
nucleus accumbens	UBERON:0001882	89.80	gold quality
frontal cortex	UBERON:0001870	89.13	gold quality
neocortex	UBERON:0001950	89.00	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.96	gold quality
anterior cingulate cortex	UBERON:0009835	88.94	gold quality
caudate nucleus	UBERON:0001873	88.84	gold quality
amygdala	UBERON:0001876	88.76	gold quality
putamen	UBERON:0001874	88.68	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.58	gold quality
cerebral cortex	UBERON:0000956	88.48	gold quality
primary visual cortex	UBERON:0002436	88.42	gold quality
Ammon’s horn	UBERON:0001954	88.09	gold quality
temporal lobe	UBERON:0001871	87.69	gold quality
spinal cord	UBERON:0002240	87.52	gold quality
right frontal lobe	UBERON:0002810	87.50	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	56.91
E-GEOD-137537	yes	14.32
E-MTAB-6678	yes	12.43
E-ENAD-17	no	1103.89
E-CURD-135	no	905.03
E-GEOD-81383	no	21.27
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPG, HR, NR1I3, TP53, TP63

miRNA regulators (miRDB)

390 targeting SGIP1, 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-8485	100.00	77.57	4731
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-520D-5P	99.98	73.34	4883

Literature-anchored findings (GeneRIF, showing 8)

• SGIP1alpha plays an essential role in clathrin-mediated endocytosis by interacting with phospholipids and Eps15. (PMID:17626015)
• SGIP1 and the signaling adaptor Reps1 interact with ITSN1 in vivo. (PMID:20946875)
• The earlier implicated single nucleotide polymorphisms located in SGIP1 gene showed no association with alcohol dependence or theta electroencephalogram power. (PMID:21317682)
• Our results show association between genetic variants in SGIP1 and fat mass. We provide evidence that variation in SGIP1 is a potentially important determinant of obesity-related traits in humans (PMID:21407171)
• crystal structures of the SGIP1 mu homology domains in complex with peptides containing two DPF motifs, are reported. (PMID:26822536)
• The present study demonstrated a possible association of target P300 evoked theta and of alcohol dependence with SNPs from the gene SGIP1 in the region of rs10889635, but further studies are required. (PMID:28030933)
• Data indicate that cysteine C632 residue is important for the function of SH3 domain GRB2 like endophilin interacting protein 1 (SGIP1) during cellular endocytosis. (PMID:30236986)
• Plasma SGIP1 methylation in diagnosis and prognosis prediction in hepatocellular carcinoma. (PMID:33118832)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	sgip1a	ENSDARG00000097897
danio_rerio	sgip1b	ENSDARG00000101215
mus_musculus	Sgip1	ENSMUSG00000028524
rattus_norvegicus	Sgip1	ENSRNOG00000006357
drosophila_melanogaster	CG8176	FBGN0037702
caenorhabditis_elegans		WBGENE00018974

Paralogs (5): GAS7 (ENSG00000007237), FCHO1 (ENSG00000130475), PSTPIP1 (ENSG00000140368), PSTPIP2 (ENSG00000152229), FCHO2 (ENSG00000157107)

Protein

Protein identifiers

SH3-containing GRB2-like protein 3-interacting protein 1 — Q9BQI5 (reviewed: Q9BQI5)

Alternative names: Endophilin-3-interacting protein

All UniProt accessions (25): A0A804HHV6, A0A804HHX3, A0A804HHZ7, A0A804HI01, A0A804HI53, A0A804HIA5, A0A804HIL8, A0A804HIL9, A0A804HIP4, A0A804HIU6, A0A804HIX4, A0A804HJ90, A0A804HJA8, A0A804HJG4, A0A804HJI3, A0A804HJJ5, A0A804HJS7, A0A804HJX5, A0A804HK43, A0A804HKA0, A0A804HKB1, A0A804HKQ5, A0A804HL75, Q9BQI5, F6R8P8

UniProt curated annotations — full annotation on UniProt →

Function. May function in clathrin-mediated endocytosis. Has both a membrane binding/tubulating activity and the ability to recruit proteins essential to the formation of functional clathrin-coated pits. Has a preference for membranes enriched in phosphatidylserine and phosphoinositides and is required for the endocytosis of the transferrin receptor. May also bind tubulin. May play a role in the regulation of energy homeostasis.

Subunit / interactions. Interacts with proteins essential or regulating the formation of functional clathrin-coated pits. Interacts with CANX. Interacts with AP2A1. Interacts with EPS15. Interacts with SH3GL3. Interacts with AMPH. Interacts with ITSN1 (via SH3 domains). Interacts with and REPS1.

Subcellular location. Membrane. Clathrin-coated pit.

Tissue specificity. Specifically expressed in brain.

Polymorphism. Genetic variation in SGIP1 is associated with fat mass and SGIP1 may be a determinant of obesity-related traits.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9BQI5-1	1	yes
Q9BQI5-2	2
Q9BQI5-3	3
Q9BQI5-4	4
Q9BQI5-5	5

RefSeq proteins (27): NP_001295132, NP_001337146, NP_001337147, NP_001363463, NP_001363464, NP_001363465, NP_001363466, NP_001363467, NP_001363468, NP_001363469, NP_001363470, NP_001363471, NP_001363472, NP_001363473, NP_001363474, NP_001363475, NP_001363476, NP_001363477, NP_001363478, NP_001363479, NP_001363480, NP_001363481, NP_001363483, NP_001363484, NP_001363485, NP_001363486, NP_115667* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018808	Muniscin_C	Domain
IPR028565	MHD	Domain
IPR036168	AP2_Mu_C_sf	Homologous_superfamily
IPR037984	SGIP1_MHD	Domain

Pfam: PF10291

UniProt features (86 total): modified residue 24, strand 18, region of interest 9, compositionally biased region 9, splice variant 6, helix 5, turn 5, sequence variant 4, sequence conflict 4, chain 1, domain 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
5AWS	X-RAY DIFFRACTION	2
5AWR	X-RAY DIFFRACTION	2.5
5AWU	X-RAY DIFFRACTION	2.7
6A9Y	X-RAY DIFFRACTION	2.7
5AWT	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQI5-F1	61.00	0.30

Functional residue map

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

Post-translational modifications (24): 78, 104, 105, 107, 149, 151, 156, 169, 180, 182, 236, 247, 259, 265, 287, 300, 316, 319, 324, 328 …

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-8856825	Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828	Clathrin-mediated endocytosis
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport

MSigDB gene sets: 339 (showing top): ATF_B, MYOGENIN_Q6, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, GOBP_BEHAVIOR, GOBP_RESPONSE_TO_DIETARY_EXCESS, GCAAGGA_MIR502, CREBP1_Q2, RACCACAR_AML_Q6, GOBP_POSITIVE_REGULATION_OF_BEHAVIOR, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_POSITIVE_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS, AATGGAG_MIR136, CAGCTG_AP4_Q5

GO Biological Process (7): response to dietary excess (GO:0002021), positive regulation of receptor-mediated endocytosis (GO:0048260), synaptic vesicle endocytosis (GO:0048488), clathrin-dependent endocytosis (GO:0072583), energy homeostasis (GO:0097009), positive regulation of feeding behavior (GO:2000253), endocytosis (GO:0006897)

GO Molecular Function (5): phospholipid binding (GO:0005543), microtubule binding (GO:0008017), SH3 domain binding (GO:0017124), protein binding (GO:0005515), tubulin binding (GO:0015631)

GO Cellular Component (9): cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), clathrin-coated pit (GO:0005905), AP-2 adaptor complex (GO:0030122), clathrin-coated vesicle (GO:0030136), presynapse (GO:0098793), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Clathrin-mediated endocytosis	1
Membrane Trafficking	1
Vesicle-mediated transport	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
receptor-mediated endocytosis	2
membrane	2
response to nutrient levels	1
energy homeostasis	1
positive regulation of endocytosis	1
regulation of receptor-mediated endocytosis	1
synaptic vesicle recycling	1
presynaptic endocytosis	1
multicellular organismal-level homeostasis	1
feeding behavior	1
positive regulation of behavior	1
regulation of feeding behavior	1
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
lipid binding	1
tubulin binding	1
protein domain specific binding	1
binding	1
cytoskeletal protein binding	1
intracellular anatomical structure	1
cytoplasm	1
cell periphery	1
endomembrane system	1
clathrin coat of endocytic vesicle	1
clathrin adaptor complex	1
clathrin coat of coated pit	1
plasma membrane protein complex	1
coated vesicle	1
synapse	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

1638 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SGIP1	EPS15	P42566	859
SGIP1	GRB2	P29354	739
SGIP1	AP2A1	O95782	730
SGIP1	AMPH	P49418	692
SGIP1	BIN1	O00499	670
SGIP1	SH3GL2	Q99962	656
SGIP1	SYNJ1	O43426	632
SGIP1	ITSN1	Q15811	615
SGIP1	SH3GL3	Q99963	596
SGIP1	DNM1	Q05193	565
SGIP1	EPS15L1	Q9UBC2	552
SGIP1	STON2	Q8WXE9	539
SGIP1	ITSN2	Q9NZM3	534
SGIP1	RHAG	Q02094	498
SGIP1	GORASP2	Q9H8Y8	435
SGIP1	NECAP1	Q8NC96	435

IntAct

13 interactions, top by confidence:

A	B	Type	Score
WLS	SGIP1	psi-mi:“MI:0915”(physical association)	0.510
SGIP1	MATR3	psi-mi:“MI:0915”(physical association)	0.400
SGIP1		psi-mi:“MI:0915”(physical association)	0.370
PRNP	WDR91	psi-mi:“MI:0914”(association)	0.350
SGIP1	AP2A2	psi-mi:“MI:0914”(association)	0.350
RHOB	RAP1GDS1	psi-mi:“MI:0914”(association)	0.350
SGIP1	SPAG6	psi-mi:“MI:0914”(association)	0.350
VCP	SHTN1	psi-mi:“MI:0914”(association)	0.350
VCP	FAM171A2	psi-mi:“MI:0914”(association)	0.350
SGIP1	PHB1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (45): SGIP1 (Reconstituted Complex), SGIP1 (Reconstituted Complex), SGIP1 (Co-crystal Structure), EPS15 (Reconstituted Complex), EPS15L1 (Reconstituted Complex), ITSN1 (Reconstituted Complex), DAB2 (Reconstituted Complex), SGIP1 (Synthetic Lethality), SGIP1 (Proximity Label-MS), SGIP1 (Affinity Capture-MS), AP2A1 (Affinity Capture-MS), AP2S1 (Affinity Capture-MS), AP2M1 (Affinity Capture-MS), EPS15L1 (Affinity Capture-MS), ITSN1 (Affinity Capture-MS)

ESM2 similar proteins: A0M8S4, A4IG59, B2RYF7, B7WN72, F1M3L7, O08719, O14964, O75061, O95208, P0DJJ3, P42768, P50551, P50552, P70315, P70429, P70460, Q03173, Q07DW4, Q07DY4, Q07E41, Q08509, Q09YJ3, Q0V8S0, Q108T9, Q12929, Q27974, Q2IBE6, Q2QLF8, Q2TA49, Q5R4H4, Q5R896, Q5RDL3, Q5RHY1, Q5ZKA6, Q64GL0, Q68FU8, Q6DCV1, Q6IZA3, Q7Z5R6, Q80TZ3

Diamond homologs: D3ZYR1, E7FBF7, O14526, P0DJJ3, Q0JRZ9, Q3UQN2, Q502I9, Q5R807, Q5RDL3, Q6IZA3, Q8K285, Q8VD37, Q9BQI5, O55148, O60861

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	120
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4849 predictions. Top by Δscore:

Variant	Effect	Δscore
1:66639765:A:G	acceptor_gain	1.0000
1:66639834:G:GG	donor_gain	1.0000
1:66642804:TTATA:T	acceptor_loss	1.0000
1:66642805:TATAG:T	acceptor_loss	1.0000
1:66642806:ATAG:A	acceptor_loss	1.0000
1:66642808:A:AG	acceptor_gain	1.0000
1:66642808:A:G	acceptor_loss	1.0000
1:66642809:G:GG	acceptor_gain	1.0000
1:66643474:A:AG	acceptor_gain	1.0000
1:66643717:GTG:G	donor_gain	1.0000
1:66679676:A:AG	acceptor_gain	1.0000
1:66679677:G:GG	acceptor_gain	1.0000
1:66679677:GC:G	acceptor_gain	1.0000
1:66679677:GCAC:G	acceptor_gain	1.0000
1:66719402:GCAA:G	donor_gain	1.0000
1:66719406:G:GG	donor_gain	1.0000
1:66729246:T:TA	acceptor_gain	1.0000
1:66729253:T:A	acceptor_gain	1.0000
1:66739321:T:A	acceptor_gain	1.0000
1:66739324:C:A	acceptor_gain	1.0000
1:66739328:C:A	acceptor_gain	1.0000
1:66739533:GTCTG:G	donor_gain	1.0000
1:66739538:G:GG	donor_gain	1.0000
1:66739538:GTATG:G	donor_loss	1.0000
1:66739539:T:G	donor_loss	1.0000
1:66740720:G:GT	donor_gain	1.0000
1:66740720:GAGGT:G	donor_loss	1.0000
1:66740721:AG:A	donor_loss	1.0000
1:66740722:GG:G	donor_loss	1.0000
1:66740723:GTAAT:G	donor_loss	1.0000

AlphaMissense

5339 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:66719305:G:A	G548R	1.000
1:66719305:G:C	G548R	1.000
1:66719306:G:A	G548E	1.000
1:66719311:A:C	S550R	1.000
1:66719313:C:A	S550R	1.000
1:66719313:C:G	S550R	1.000
1:66719345:C:A	P561H	1.000
1:66719348:T:A	V562D	1.000
1:66719351:C:A	A563E	1.000
1:66729298:T:C	S593P	1.000
1:66729302:T:C	F594S	1.000
1:66729305:C:A	P595H	1.000
1:66729305:C:G	P595R	1.000
1:66729308:C:A	A596D	1.000
1:66729310:G:C	G597R	1.000
1:66729311:G:A	G597D	1.000
1:66729326:T:C	F602S	1.000
1:66729359:T:C	F613S	1.000
1:66729410:T:C	L630P	1.000
1:66733804:T:C	L652S	1.000
1:66733804:T:G	L652W	1.000
1:66733816:T:A	L656Q	1.000
1:66733816:T:C	L656P	1.000
1:66733851:T:C	Y668H	1.000
1:66733851:T:G	Y668D	1.000
1:66733854:T:G	Y669D	1.000
1:66733859:C:A	N670K	1.000
1:66733859:C:G	N670K	1.000
1:66733861:T:A	V671D	1.000
1:66733870:T:C	L674P	1.000

dbSNP variants (sampled 300 via entrez): RS1000020074 (1:66571236 A>G), RS1000021957 (1:66593093 G>A,C), RS1000055697 (1:66747956 G>A), RS1000067061 (1:66631713 C>A,T), RS1000075939 (1:66708483 G>A,C), RS1000092183 (1:66742040 A>G), RS1000092720 (1:66586678 T>C), RS1000112392 (1:66715520 C>T), RS1000133955 (1:66633134 C>T), RS1000135965 (1:66664531 C>CTG), RS1000152934 (1:66751192 C>A,T), RS1000162313 (1:66583098 T>C), RS1000171265 (1:66622621 T>A,G), RS1000177887 (1:66680727 C>A), RS1000179525 (1:66565807 A>G,T)

Disease associations

OMIM: gene MIM:611540 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

86 associations (top):

Study	Trait	p-value
GCST001810_1	Menopause (age at onset)	5.000000e-06
GCST001872_2	Presence of antiphospholipid antibodies	7.000000e-06
GCST004131_16	Inflammatory bowel disease	5.000000e-111
GCST004132_7	Crohn’s disease	6.000000e-93
GCST004133_2	Ulcerative colitis	4.000000e-41
GCST004490_6	Cerebrospinal fluid t-tau:AB1-42 ratio	3.000000e-08
GCST006629_49	Pulse pressure	5.000000e-14
GCST006979_980	Heel bone mineral density	6.000000e-16
GCST007267_81	Systolic blood pressure	5.000000e-10
GCST007269_23	Pulse pressure	1.000000e-09
GCST007329_2	Automobile speeding propensity	8.000000e-11
GCST007576_66	Chronotype	5.000000e-09
GCST009254_1	Cerebellum white matter volume	8.000000e-06
GCST009524_87	Household income (MTAG)	2.000000e-08
GCST010346_29	TPE interval (resting)	8.000000e-18
GCST010346_32	TPE interval (resting)	3.000000e-20
GCST010796_126	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-12
GCST010796_127	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14
GCST010796_128	Electrocardiogram morphology (amplitude at temporal datapoints)	9.000000e-15
GCST010796_129	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14
GCST010796_130	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-16
GCST010796_131	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-16
GCST010796_132	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14
GCST010796_133	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14
GCST010796_134	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14
GCST010796_135	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-14
GCST010796_136	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14
GCST010796_137	Electrocardiogram morphology (amplitude at temporal datapoints)	7.000000e-15
GCST010796_138	Electrocardiogram morphology (amplitude at temporal datapoints)	2.000000e-14
GCST010796_139	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-14

EFO canonical traits (11, from GWAS)

EFO ID	Trait name
EFO:0004704	age at menopause
EFO:0007708	t-tau:beta-amyloid 1-42 ratio measurement
EFO:0005763	pulse pressure measurement
EFO:0009270	heel bone mineral density
EFO:0006335	systolic blood pressure
EFO:0008579	risk-taking behaviour
EFO:0008328	chronotype measurement
EFO:0008320	white matter volume measurement
EFO:0009695	household income
EFO:0004644	TPE interval measurement
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs12402181	MIR3117, SGIP1		0.00	0

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Doxorubicin	increases expression, decreases expression	2
Valproic Acid	increases expression	2
bisphenol A	affects methylation	1
arsenite	increases methylation	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
incobotulinumtoxinA	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Cytarabine	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Oxygen	increases expression	1
Progesterone	affects cotreatment, decreases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression	1
Mifepristone	increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	increases abundance, decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D6S5	SCTCi034-A	Induced pluripotent stem cell	Female
CVCL_D6S6	SCTCi035-A	Induced pluripotent stem cell	Female

Clinical trials (associated diseases)

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