SVEP1

Summary

SVEP1 (sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1, HGNC:15985) is a protein-coding gene on chromosome 9q31.3, encoding Sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 (Q4LDE5). Required for morphological development, cell alignment and migration of lymphatic endothelial cells during embryonic development, potentially via modulation of ANGPT2-TIE1 signaling and subsequent activation of FOXC2 transcription.

Enables integrin binding activity. Involved in negative regulation of vasoconstriction and positive regulation of platelet activation. Located in cytoplasm and nucleus.

Source: NCBI Gene 79987 — RefSeq curated summary.

At a glance

• GWAS associations: 25
• Clinical variants (ClinVar): 543 total
• MANE Select transcript: NM_153366

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15985
Approved symbol	SVEP1
Name	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1
Location	9q31.3
Locus type	gene with protein product
Status	Approved
Aliases	bA427L11.3, POLYDOM, FLJ13529
Ensembl gene	ENSG00000165124
Ensembl biotype	protein_coding
OMIM	611691
Entrez	79987

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000374461, ENST00000374469, ENST00000467821, ENST00000476205

RefSeq mRNA: 1 — MANE Select: NM_153366 NM_153366

CCDS: CCDS48004

Canonical transcript exons

ENST00000374469 — 48 exons

Exon	Start	End
ENSE00001224788	110549849	110550104
ENSE00001224970	110443545	110443720
ENSE00001463598	110365248	110366560
ENSE00001463644	110436380	110436504
ENSE00001463666	110579013	110579741
ENSE00001609345	110389524	110389587
ENSE00001611624	110430274	110430450
ENSE00001611730	110432462	110432635
ENSE00001626528	110404327	110404552
ENSE00001627383	110377271	110377366
ENSE00001632650	110431915	110432034
ENSE00001644783	110375368	110375463
ENSE00001656254	110369923	110370016
ENSE00001659510	110406160	110408951
ENSE00001659872	110385898	110386074
ENSE00001675145	110429920	110430004
ENSE00001691759	110387285	110387458
ENSE00001739651	110429143	110429334
ENSE00001746441	110379347	110379517
ENSE00001770527	110400854	110401009
ENSE00001774728	110434336	110434506
ENSE00001790505	110435241	110435364
ENSE00003471210	110503038	110503217
ENSE00003481190	110513948	110514106
ENSE00003486910	110451289	110451402
ENSE00003501152	110479635	110479756
ENSE00003501621	110546115	110546291
ENSE00003513530	110472159	110472323
ENSE00003519709	110489650	110489779
ENSE00003523038	110427591	110427758
ENSE00003527086	110445837	110446038
ENSE00003542232	110482361	110482492
ENSE00003557591	110450059	110450260
ENSE00003562442	110465865	110466026
ENSE00003562940	110481242	110481436
ENSE00003570423	110476204	110476315
ENSE00003571504	110468940	110469101
ENSE00003582857	110411063	110411735
ENSE00003611942	110471364	110471597
ENSE00003620087	110512926	110513105
ENSE00003636707	110483586	110483693
ENSE00003640316	110457256	110457352
ENSE00003648366	110446900	110447057
ENSE00003684815	110455590	110455703
ENSE00003686411	110458952	110459113
ENSE00003688541	110458471	110458562
ENSE00003691814	110499041	110499238
ENSE00003692705	110496815	110496933

Expression profiles

Bgee: expression breadth ubiquitous, 225 present calls, max score 97.07.

FANTOM5 (CAGE): breadth broad, TPM avg 5.8627 / max 553.3168, expressed in 773 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
101932	2.0871	488
101930	1.2035	461
101935	0.6499	234
101931	0.3505	169
101937	0.3363	159
101939	0.3113	116
101929	0.3011	183
101934	0.2995	135
101938	0.2102	92
101936	0.0542	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pericardium	UBERON:0002407	97.07	gold quality
lower lobe of lung	UBERON:0008949	94.59	gold quality
placenta	UBERON:0001987	93.66	gold quality
skin of hip	UBERON:0001554	92.77	gold quality
parietal pleura	UBERON:0002400	92.68	gold quality
superficial temporal artery	UBERON:0001614	92.40	gold quality
germinal epithelium of ovary	UBERON:0001304	91.92	gold quality
omental fat pad	UBERON:0010414	91.88	gold quality
adipose tissue of abdominal region	UBERON:0007808	91.86	gold quality
peritoneum	UBERON:0002358	91.85	gold quality
adipose tissue	UBERON:0001013	91.68	gold quality
secondary oocyte	CL:0000655	91.22	gold quality
connective tissue	UBERON:0002384	91.15	gold quality
subcutaneous adipose tissue	UBERON:0002190	91.02	gold quality
thoracic mammary gland	UBERON:0005200	89.21	gold quality
right lung	UBERON:0002167	89.18	gold quality
pleura	UBERON:0000977	89.13	gold quality
mammary gland	UBERON:0001911	89.02	gold quality
mammary duct	UBERON:0001765	88.55	gold quality
stromal cell of endometrium	CL:0002255	87.83	gold quality
vena cava	UBERON:0004087	87.62	silver quality
epithelium of mammary gland	UBERON:0003244	87.26	gold quality
colonic epithelium	UBERON:0000397	87.18	gold quality
lung	UBERON:0002048	87.17	gold quality
cardia of stomach	UBERON:0001162	86.79	gold quality
saphenous vein	UBERON:0007318	86.47	gold quality
oocyte	CL:0000023	86.01	gold quality
upper lobe of lung	UBERON:0008948	85.90	gold quality
upper lobe of left lung	UBERON:0008952	85.85	gold quality
synovial joint	UBERON:0002217	85.72	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	33.28
E-MTAB-9543	yes	15.03
E-CURD-119	yes	11.24
E-MTAB-9388	yes	10.80
E-GEOD-81547	yes	8.10
E-MTAB-6678	yes	3.98
E-CURD-10	no	38.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

72 targeting SVEP1, 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-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-6079	99.84	68.54	1170
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-466	99.67	70.85	2863

Literature-anchored findings (GeneRIF, showing 20)

• All together makes SEL-OB/SVEP1 an attractive marker for studying the role of stromal osteogenic cells and their interactions within the bone marrow microenvironment creating a network that regulates the skeletal homeostasis. (PMID:16206243)
• acts as regulator of ICAM1 and E-selectin during endotoxemia (PMID:20236627)
• Increased UT-II, sTM, and vWF in ankylosing spondylitis patient sera regardless of treatment and disease activity suggest an increased tendency for atherosclerosis. (PMID:21556780)
• polydom is a hitherto unknown ligand for integrin alpha9beta1 that functions as a physiological ligand in vivo. (PMID:22654117)
• c.2080A>C SNP associated with increased 28-day mortality in septic shock (PMID:25188548)
• We also found significant associations between coronary artery disease and low-frequency missense variants in the genes SVEP1. (PMID:26934567)
• Top association findings suggested that the bipolar disorder risk allele at SNP rs7042161 in SVEP1 gene may be associated with increased risk of essential hypertension. (PMID:27529678)
• Downregulation of SVEP1 expression in primary keratinocytes resulted in decreased expression of major epidermal differentiation markers. (PMID:27892606)
• increased polydom expression in the dermis surrounding neurofibromas may promote dermal neurofibroma development by activating TGF-beta1 (PMID:31570272)
• The novel miR-1269b-regulated protein SVEP1 induces hepatocellular carcinoma proliferation and metastasis likely through the PI3K/Akt pathway. (PMID:32371982)
• SVEP1 as a Genetic Modifier of TEK-Related Primary Congenital Glaucoma. (PMID:33027505)
• Functional investigation of the coronary artery disease gene SVEP1. (PMID:33185739)
• SVEP1 is a human coronary artery disease locus that promotes atherosclerosis. (PMID:33762433)
• A genome-wide association study identifying SVEP1 variant as a predictor of response to tolvaptan for cirrhotic ascites. (PMID:34309184)
• SVEP1 is important for morphogenesis of lymphatic system: Possible implications in lymphedema. (PMID:34506084)
• Effects of SVEP1 on Lung Squamous Cell Carcinoma and its Association with Tumor Mutation Burden, Prognosis, and Immune Regulation. (PMID:35306983)
• The integrin ligand SVEP1 regulates GPCR-mediated vasoconstriction via integrins alpha9beta1 and alpha4beta1. (PMID:35802072)
• Decreased expression of SVEP1 is closely related to a cancer stem cell-like phenotype and poor prognosis in hepatocellular carcinoma. (PMID:35900319)
• SVEP1 influences monocyte to macrophage differentiation via integrin alpha4beta1/alpha9beta1 and Rho/Rac signalling. (PMID:37100352)
• EGR1 transcriptionally regulates SVEP1 to promote proliferation and migration in human coronary artery smooth muscle cells. (PMID:38409611)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	svep1	ENSDARG00000013526
mus_musculus	Svep1	ENSMUSG00000028369
rattus_norvegicus	Svep1	ENSRNOG00000033110

Paralogs (39): CFH (ENSG00000000971), SELE (ENSG00000007908), C8B (ENSG00000021852), C6 (ENSG00000039537), SEZ6 (ENSG00000063015), CFHR2 (ENSG00000080910), APOH (ENSG00000091583), SEZ6L (ENSG00000100095), SUSD6 (ENSG00000100647), SRPX (ENSG00000101955), SRPX2 (ENSG00000102359), C7 (ENSG00000112936), C9 (ENSG00000113600), PAPPA2 (ENSG00000116183), CFHR3 (ENSG00000116785), CR2 (ENSG00000117322), CD46 (ENSG00000117335), CSMD2 (ENSG00000121904), C4BPA (ENSG00000123838), C4BPB (ENSG00000123843), CFHR4 (ENSG00000134365), CFHR5 (ENSG00000134389), F13B (ENSG00000143278), SUSD4 (ENSG00000143502), C8A (ENSG00000157131), SUSD3 (ENSG00000157303), CSMD3 (ENSG00000164796), C2 (ENSG00000166278), SELP (ENSG00000174175), SEZ6L2 (ENSG00000174938), PRF1 (ENSG00000180644), PAPPA (ENSG00000182752), CSMD1 (ENSG00000183117), SELL (ENSG00000188404), CD55 (ENSG00000196352), CR1L (ENSG00000197721), CR1 (ENSG00000203710), CFB (ENSG00000243649), CFHR1 (ENSG00000244414)

Protein

Protein identifiers

Sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1 — Q4LDE5 (reviewed: Q4LDE5)

Alternative names: CCP module-containing protein 22, Polydom, Selectin-like osteoblast-derived protein, Serologically defined breast cancer antigen NY-BR-38

All UniProt accessions (1): Q4LDE5

UniProt curated annotations — full annotation on UniProt →

Function. Required for morphological development, cell alignment and migration of lymphatic endothelial cells during embryonic development, potentially via modulation of ANGPT2-TIE1 signaling and subsequent activation of FOXC2 transcription. Required for embryonic lymphatic vascular development, via mediating the correct formation of the first lymphovenous contact site and tight association of the lymphatic endothelium with the venous endothelium. Represses PRKCA-mediated L-type voltage-gated channel Ca(2+) influx and ROCK-mediated calcium sensitivity in vascular smooth muscle cells, via its interaction with integrins, thereby inhibiting vasocontraction. Promotes platelet activation, via its interaction with PEAR1 and subsequent activation of AKT/mTOR signaling. Plays a role in epidermal development and keratinocyte differentiation, independent of cell-cell adhesion. May play a role in initial cell attachment of stromal osteogenic cells. May promote myoblast cell adhesion when in the presence of integrin ITGA9:ITGB1.

Subunit / interactions. Interacts (via Sushi domain 21) with ITGA9:ITGB1; thereby inhibits Ca(2+) intracellular signaling and as a result represses vasocontraction. Interacts (via Sushi domain 21) with ITGA4:ITGB1; thereby inhibits Ca(2+) intracellular signaling and as a result represses vasocontraction. Interacts with ANGPT1 and ANGPT2. Interacts with PEAR1 (via extracellular domain). Interacts with HSPG2, TLN1, FN1, COPA, CCT2, IQGAP1, LAMC1 and NID1. Interacts (via C-terminus) with TIE1.

Subcellular location. Secreted. Nucleus. Cytoplasm. Membrane.

Tissue specificity. Expressed in mesenchymal cells (at protein level). Expressed in vascular smooth muscle cells (at protein level). Expressed throughout the epidermis, expression is most prominent in the basal and lower suprabasal layers of the epidermis and in dermal fibroblasts in the upper dermis (at protein level). Abundantly expressed in the placenta, weakly expressed in heart and skeletal muscle. Also expressed in the lung, adrenal gland and cerebellum.

Post-translational modifications. O-glycosylated with core 1 or possibly core 8 glycans.

Isoforms (4)

UniProt ID	Names	Canonical?
Q4LDE5-1	1	yes
Q4LDE5-2	2
Q4LDE5-3	3
Q4LDE5-4	4

RefSeq proteins (1): NP_699197* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000152	EGF-type_Asp/Asn_hydroxyl_site	PTM
IPR000436	Sushi_SCR_CCP_dom	Domain
IPR000742	EGF	Domain
IPR001759	PTX_dom	Domain
IPR001881	EGF-like_Ca-bd_dom	Domain
IPR002035	VWF_A	Domain
IPR003410	HYR_dom	Domain
IPR009030	Growth_fac_rcpt_cys_sf	Homologous_superfamily
IPR011641	Tyr-kin_ephrin_A/B_rcpt-like	Domain
IPR013032	EGF-like_CS	Conserved_site
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR018097	EGF_Ca-bd_CS	Conserved_site
IPR035976	Sushi/SCR/CCP_sf	Homologous_superfamily
IPR036465	vWFA_dom_sf	Homologous_superfamily
IPR049883	NOTCH1_EGF-like	Domain
IPR050350	Compl-Cell_Adhes-Reg	Family

Pfam: PF00008, PF00084, PF00092, PF00354, PF02494, PF07645, PF07699, PF12661

UniProt features (202 total): disulfide bond 93, domain 47, sequence conflict 28, sequence variant 19, glycosylation site 5, splice variant 4, region of interest 2, signal peptide 1, chain 1, short sequence motif 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q4LDE5 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

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): 2642 (required for interaction with integrin itga9:itgb1)

Disulfide bonds (93): 2047–2078, 2083–2126, 2112–2141, 2146–2186, 2172–2199, 2204–2245, 2231–2259, 2264–2304, 2290–2318, 2323–2363, 2349–2376, 2381–2422, 2408–2435, 2440–2480, 2466–2493, 2498–2538, 2524–2551, 2556–2596, 2582–2608, 2685–2712 …

Glycosylation sites (5): 186, 847, 1102, 3018, 3186

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 147 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, MODULE_169, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_PLATELET_ACTIVATION, GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP, GOBP_WOUND_HEALING, BROWNE_HCMV_INFECTION_48HR_DN, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_CELL_JUNCTION_ORGANIZATION, RIGGI_EWING_SARCOMA_PROGENITOR_DN, GOBP_POSITIVE_REGULATION_OF_CELL_ACTIVATION, THUM_MIR21_TARGETS_HEART_DISEASE_UP, GNF2_KISS1

GO Biological Process (13): lymph circulation (GO:0003017), epidermis development (GO:0008544), gene expression (GO:0010467), positive regulation of platelet activation (GO:0010572), lymph vessel morphogenesis (GO:0036303), negative regulation of vasoconstriction (GO:0045906), Tie signaling pathway (GO:0048014), tight junction organization (GO:0120193), lymph vessel development (GO:0001945), circulatory system process (GO:0003013), cell adhesion (GO:0007155), cell-matrix adhesion (GO:0007160), negative regulation of multicellular organismal process (GO:0051241)

GO Molecular Function (5): chromatin binding (GO:0003682), integrin binding (GO:0005178), calcium ion binding (GO:0005509), integrin binding involved in cell-matrix adhesion (GO:0098640), protein binding (GO:0005515)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), nucleus (GO:0005634), cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	2
circulatory system process	1
tissue development	1
macromolecule biosynthetic process	1
regulation of platelet activation	1
platelet activation	1
positive regulation of cell activation	1
lymph vessel development	1
anatomical structure morphogenesis	1
regulation of vasoconstriction	1
vasoconstriction	1
negative regulation of multicellular organismal process	1
cell surface receptor protein tyrosine kinase signaling pathway	1
cell-cell junction organization	1
vasculature development	1
anatomical structure development	1
system process	1
cellular process	1
cell-substrate adhesion	1
multicellular organismal process	1
negative regulation of biological process	1
regulation of multicellular organismal process	1
signaling receptor binding	1
protein-containing complex binding	1
cell adhesion molecule binding	1
metal ion binding	1
integrin binding	1
cell-matrix adhesion	1
cell-matrix adhesion mediator activity	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

2233 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SVEP1	VWF	P04275	832
SVEP1	ANGPT2	O15123	552
SVEP1	EGF	P01133	544
SVEP1	ITGA9	Q13797	445
SVEP1	GCC2	Q8IWJ2	440
SVEP1	RAMP2	O60895	432
SVEP1	MPHOSPH6	Q99547	423
SVEP1	PSG4	Q00888	380
SVEP1	RAG1	P15918	365
SVEP1	SELP	P16109	359
SVEP1	BMP4	P12644	354
SVEP1	MAOA	P21397	353
SVEP1	ASPM	Q8IZT6	353
SVEP1	MEIS1	O00470	348
SVEP1	PANX2	Q96RD6	340

IntAct

16 interactions, top by confidence:

A	B	Type	Score
SVEP1	yscK	psi-mi:“MI:0915”(physical association)	0.370
SVEP1	sctL	psi-mi:“MI:0915”(physical association)	0.370
SKIL	SVEP1	psi-mi:“MI:0915”(physical association)	0.370
SMAD3	SVEP1	psi-mi:“MI:0915”(physical association)	0.370
ATF7IP	SVEP1	psi-mi:“MI:0915”(physical association)	0.370
ZFYVE9	SVEP1	psi-mi:“MI:0915”(physical association)	0.370
SMAD9	SVEP1	psi-mi:“MI:0915”(physical association)	0.370
SVEP1		psi-mi:“MI:0915”(physical association)	0.370
MTNR1A	SVEP1	psi-mi:“MI:0915”(physical association)	0.000
SVEP1	groEL	psi-mi:“MI:0915”(physical association)	0.000
	SVEP1	psi-mi:“MI:0915”(physical association)	0.000
rfbD	SVEP1	psi-mi:“MI:0915”(physical association)	0.000
cdiA	SVEP1	psi-mi:“MI:0915”(physical association)	0.000
SVEP1	ddg	psi-mi:“MI:0915”(physical association)	0.000
SVEP1		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): SVEP1 (Two-hybrid), SVEP1 (Affinity Capture-RNA), SVEP1 (Affinity Capture-MS), SVEP1 (Proximity Label-MS), SVEP1 (Proximity Label-MS), SVEP1 (Two-hybrid), ABCB5 (Cross-Linking-MS (XL-MS)), SVEP1 (Cross-Linking-MS (XL-MS)), SVEP1 (Two-hybrid), SVEP1 (Two-hybrid), SVEP1 (Two-hybrid), SVEP1 (Two-hybrid)

ESM2 similar proteins: A0A1D5NSM8, A2AVA0, B1AUH1, B3DK56, D3ZHH1, E9Q6D8, G5E8Q8, O18016, O97827, P0C6B8, P13671, P21180, P28175, P35442, P35918, P61134, P61135, P86091, Q03350, Q05793, Q08E66, Q26422, Q29RU4, Q2QI47, Q4LDE5, Q5E9P5, Q5G872, Q5MD89, Q5RDI1, Q6DI48, Q6DIV5, Q6GP28, Q6NZL8, Q6UXH9, Q6YI48, Q7RTY8, Q7TQN3, Q80TS3, Q811M5, Q8BIK6

Diamond homologs: A0A1D5NSM8, A0JNA2, A2AVA0, A2AX52, D3YXF5, O02839, O19063, O35764, O43405, O70340, O76536, O89029, O95502, O96530, P02741, P02743, P06205, P06206, P06207, P06681, P07202, P07629, P08607, P09871, P0C6B8, P10643, P12246, P13944, P14151, P14847, P15697, P18337, P23680, P32018, P47970, P47971, P47972, P48199, P49254, P49262

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	447
Likely benign	44
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

7059 predictions. Top by Δscore:

Variant	Effect	Δscore
9:110379341:CCTTA:C	donor_loss	1.0000
9:110379342:CTTA:C	donor_loss	1.0000
9:110379343:TTACC:T	donor_loss	1.0000
9:110379344:TA:T	donor_loss	1.0000
9:110379345:A:AC	donor_gain	1.0000
9:110379346:C:CA	donor_loss	1.0000
9:110379346:C:CC	donor_gain	1.0000
9:110379346:CCT:C	donor_gain	1.0000
9:110379346:CCTCT:C	donor_gain	1.0000
9:110379513:GATTT:G	acceptor_gain	1.0000
9:110379514:ATTT:A	acceptor_gain	1.0000
9:110379515:TTT:T	acceptor_gain	1.0000
9:110379515:TTTC:T	acceptor_loss	1.0000
9:110379516:TT:T	acceptor_gain	1.0000
9:110379517:TCTA:T	acceptor_loss	1.0000
9:110379518:C:CA	acceptor_loss	1.0000
9:110379518:C:CC	acceptor_gain	1.0000
9:110386071:TTTG:T	acceptor_gain	1.0000
9:110386075:C:CC	acceptor_gain	1.0000
9:110389519:CTCA:C	donor_loss	1.0000
9:110389520:TCA:T	donor_loss	1.0000
9:110389521:CA:C	donor_loss	1.0000
9:110389523:C:A	donor_loss	1.0000
9:110389585:CCC:C	acceptor_gain	1.0000
9:110389586:CC:C	acceptor_gain	1.0000
9:110389586:CCC:C	acceptor_gain	1.0000
9:110389587:CC:C	acceptor_gain	1.0000
9:110389588:C:CA	acceptor_loss	1.0000
9:110389588:C:CC	acceptor_gain	1.0000
9:110400848:GCTTA:G	donor_loss	1.0000

AlphaMissense

23493 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:110432487:C:A	W1736C	1.000
9:110432487:C:G	W1736C	1.000
9:110550049:T:A	D196V	1.000
9:110379369:C:A	W3462C	0.999
9:110379369:C:G	W3462C	0.999
9:110385923:C:A	W3404C	0.999
9:110385923:C:G	W3404C	0.999
9:110411135:C:A	W2192C	0.999
9:110411135:C:G	W2192C	0.999
9:110411154:C:G	C2186S	0.999
9:110411155:A:T	C2186S	0.999
9:110411315:C:A	W2132C	0.999
9:110411315:C:G	W2132C	0.999
9:110411317:A:G	W2132R	0.999
9:110411317:A:T	W2132R	0.999
9:110411510:C:A	W2067C	0.999
9:110411510:C:G	W2067C	0.999
9:110411684:C:A	W2009C	0.999
9:110411684:C:G	W2009C	0.999
9:110432506:C:G	C1730S	0.999
9:110432507:A:T	C1730S	0.999
9:110432548:C:G	C1716S	0.999
9:110432549:A:T	C1716S	0.999
9:110503063:C:A	W486C	0.999
9:110503063:C:G	W486C	0.999
9:110550048:A:C	D196E	0.999
9:110550048:A:T	D196E	0.999
9:110550049:T:G	D196A	0.999
9:110550058:A:G	L193P	0.999
9:110375390:C:A	W3526C	0.998

dbSNP variants (sampled 300 via entrez): RS1000063051 (9:110402820 GT>G), RS1000067455 (9:110553356 G>A,C), RS1000076314 (9:110455072 A>G), RS1000088381 (9:110539237 G>A), RS1000122178 (9:110579069 C>T), RS1000143484 (9:110559892 T>G), RS1000169057 (9:110493740 A>C), RS1000178092 (9:110428800 G>A), RS1000189019 (9:110536804 G>A), RS1000196963 (9:110365790 A>G,T), RS1000208513 (9:110577709 C>A,T), RS1000220599 (9:110569102 A>G), RS1000230328 (9:110524021 A>G), RS1000300269 (9:110451558 T>C), RS1000317518 (9:110530340 C>T)

Disease associations

OMIM: gene MIM:611691 | disease phenotypes: MIM:616325, MIM:208150

GenCC curated gene-disease

Mondo (2): congenital myasthenic syndrome 9 (MONDO:0014587), fetal akinesia deformation sequence 1 (MONDO:0100101)

Orphanet (2): Congenital myasthenic syndrome (Orphanet:590), Fetal akinesia deformation sequence (Orphanet:994)

HPO phenotypes

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

GWAS associations

25 associations (top):

Study	Trait	p-value
GCST000785_30	Longevity	1.000000e-06
GCST001843_3	Type 2 diabetes (dietary heme iron intake interaction)	1.000000e-06
GCST004616_204	Platelet distribution width	5.000000e-09
GCST004787_43	Coronary artery disease (myocardial infarction, percutaneous transluminal coronary angioplasty, coronary artery bypass grafting, angina or chromic ischemic heart disease)	8.000000e-07
GCST005196_174	Coronary artery disease	8.000000e-09
GCST006228_9	Systolic blood pressure	1.000000e-07
GCST006231_35	Mean arterial pressure	8.000000e-08
GCST006585_508	Blood protein levels	8.000000e-28
GCST006585_567	Blood protein levels	5.000000e-24
GCST006865_2	Bipolar disorder	6.000000e-06
GCST007094_46	Diastolic blood pressure	5.000000e-07
GCST007096_120	Pulse pressure	2.000000e-07
GCST007099_164	Systolic blood pressure	4.000000e-11
GCST007267_337	Systolic blood pressure	4.000000e-08
GCST007929_95	Medication use (calcium channel blockers)	2.000000e-08
GCST007930_148	Medication use (agents acting on the renin-angiotensin system)	5.000000e-10
GCST008163_84	Height	6.000000e-06
GCST008181_7	Spontaneous preterm birth without premature rupture of membranes	8.000000e-06
GCST011106_1	Metamizole-induced agranulocytosis	6.000000e-07
GCST011939_22	Takayasu arteritis	5.000000e-08
GCST90002395_57	Mean platelet volume	7.000000e-09
GCST90002395_58	Mean platelet volume	2.000000e-17
GCST90002401_492	Platelet distribution width	5.000000e-29
GCST90002402_69	Platelet count	5.000000e-12
GCST90011770_20	Glaucoma (primary open-angle)	4.000000e-08

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0008355	dietary heme iron intake measurement
EFO:0007984	platelet component distribution width
EFO:0006335	systolic blood pressure
EFO:0006340	mean arterial pressure
EFO:0006336	diastolic blood pressure
EFO:0005763	pulse pressure measurement
EFO:0009930	Calcium channel blocker use measurement
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0006917	spontaneous preterm birth
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, increases abundance, decreases expression	3
Valproic Acid	affects cotreatment, increases expression, decreases methylation	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Benzo(a)pyrene	affects methylation, increases expression	2
Dexamethasone	decreases expression, increases expression, affects cotreatment	2
Estradiol	affects cotreatment, decreases expression, affects expression	2
Phenylmercuric Acetate	increases expression, affects cotreatment	2
Tobacco Smoke Pollution	decreases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
bisphenol F	decreases expression, affects cotreatment	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
propionaldehyde	decreases expression	1
arsenite	increases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
zinc chromate	increases abundance, increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	decreases expression	1
cupric chloride	decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
pentanal	decreases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases expression, affects cotreatment	1
jinfukang	affects cotreatment, decreases expression	1
incobotulinumtoxinA	increases expression	1
Dasatinib	increases expression	1
Decitabine	decreases expression, decreases reaction	1

Clinical trials (associated diseases)

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