PSD3

Summary

PSD3 (pleckstrin and Sec7 domain containing 3, HGNC:19093) is a protein-coding gene on chromosome 8p22, encoding PH and SEC7 domain-containing protein 3 (Q9NYI0). Guanine nucleotide exchange factor for ARF6.

Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction. Predicted to be located in membrane. Predicted to be active in glutamatergic synapse; postsynapse; and ruffle membrane.

Source: NCBI Gene 23362 — RefSeq curated summary.

At a glance

• Gene–disease (curated): antecubital pterygium syndrome (Limited, ClinGen)
• GWAS associations: 48
• Clinical variants (ClinVar): 146 total
• Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
• MANE Select transcript: NM_015310

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19093
Approved symbol	PSD3
Name	pleckstrin and Sec7 domain containing 3
Location	8p22
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0942, HCA67, EFA6R, DKFZp761K1423, EFA6D
Ensembl gene	ENSG00000156011
Ensembl biotype	protein_coding
OMIM	614440
Entrez	23362

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 8 protein_coding, 4 protein_coding_CDS_not_defined, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000286485, ENST00000327040, ENST00000428502, ENST00000517971, ENST00000518303, ENST00000518315, ENST00000518963, ENST00000519633, ENST00000519653, ENST00000519851, ENST00000520789, ENST00000520858, ENST00000521027, ENST00000521475, ENST00000521841, ENST00000521878, ENST00000523619

RefSeq mRNA: 28 — MANE Select: NM_015310 NM_001362819, NM_001412865, NM_001412866, NM_001412870, NM_001412871, NM_001412872, NM_001412873, NM_001412874, NM_001412875, NM_001412876, NM_001412880, NM_001412882, NM_001412883, NM_001412884, NM_001412885, NM_001412886, NM_001412887, NM_001412888, NM_001412889, NM_001412890, NM_001412891, NM_001412892, NM_001412893, NM_001412894, NM_001412895, NM_001412896, NM_015310, NM_206909

CCDS: CCDS34854, CCDS43720

Canonical transcript exons

ENST00000327040 — 16 exons

Exon	Start	End
ENSE00001342364	18867674	18868069
ENSE00001801145	18527303	18535958
ENSE00003496966	18871626	18872733
ENSE00003498550	18804522	18804602
ENSE00003515527	18600364	18600434
ENSE00003535650	18572528	18572672
ENSE00003560798	18799295	18799353
ENSE00003564038	18575128	18575285
ENSE00003577343	18804704	18804898
ENSE00003584316	18556209	18556352
ENSE00003603525	18936034	18936142
ENSE00003662694	18632613	18632806
ENSE00003689268	18801270	18801382
ENSE00003694176	18655642	18655685
ENSE00003784120	18765449	18765538
ENSE00003848482	19013563	19013703

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 99.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.1827 / max 1435.3614, expressed in 1566 samples.

FANTOM5 promoters (23 alternative TSS)

Promoter ID	TPM avg	Samples expressed
92099	6.0905	1390
92073	4.5014	122
92098	3.7309	1218
92074	2.1190	117
92100	1.6728	890
92104	0.9244	317
92079	0.7813	82
92094	0.7746	321
92093	0.5568	273
92102	0.5546	253

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	99.59	gold quality
endothelial cell	CL:0000115	99.45	gold quality
cerebellar vermis	UBERON:0004720	99.40	gold quality
middle temporal gyrus	UBERON:0002771	99.31	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.12	gold quality
parietal lobe	UBERON:0001872	98.94	gold quality
postcentral gyrus	UBERON:0002581	98.91	gold quality
entorhinal cortex	UBERON:0002728	98.87	gold quality
calcaneal tendon	UBERON:0003701	98.82	gold quality
superior frontal gyrus	UBERON:0002661	98.56	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.51	gold quality
pons	UBERON:0000988	98.36	gold quality
orbitofrontal cortex	UBERON:0004167	98.36	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.32	gold quality
lateral globus pallidus	UBERON:0002476	98.21	gold quality
tibia	UBERON:0000979	98.03	gold quality
secondary oocyte	CL:0000655	97.93	gold quality
substantia nigra pars compacta	UBERON:0001965	97.92	gold quality
adrenal tissue	UBERON:0018303	97.81	gold quality
CA1 field of hippocampus	UBERON:0003881	97.44	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	97.38	gold quality
cartilage tissue	UBERON:0002418	97.37	gold quality
corpus callosum	UBERON:0002336	97.28	gold quality
oocyte	CL:0000023	97.12	gold quality
superior vestibular nucleus	UBERON:0007227	96.48	gold quality
dorsal plus ventral thalamus	UBERON:0001897	96.34	gold quality
medulla oblongata	UBERON:0001896	96.27	gold quality
inferior vagus X ganglion	UBERON:0005363	96.24	gold quality
subthalamic nucleus	UBERON:0001906	96.05	gold quality
tendon	UBERON:0000043	95.93	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	43.31
E-MTAB-9067	yes	13.35
E-ENAD-17	no	586.36
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

577 targeting PSD3, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 4)

• Down regulated in ovarian cancer or absent in ovarian cancer and impact survival. (PMID:16270321)
• EFA6R regulated ARF6 localization and thereby actin stress fiber loss. (PMID:25296758)
• Common variants in PSD3 were associated with obesity, T2D and HDL level (PMID:28237857)
• PSD3 downregulation confers protection against fatty liver disease. (PMID:35102341)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	psd3l	ENSDARG00000104820
mus_musculus	Psd3	ENSMUSG00000030465
rattus_norvegicus	Psd3	ENSRNOG00000013884
drosophila_melanogaster	siz	FBGN0026179
drosophila_melanogaster	Sec71	FBGN0028538
drosophila_melanogaster	garz	FBGN0264560
caenorhabditis_elegans		WBGENE00007703
caenorhabditis_elegans		WBGENE00008685
caenorhabditis_elegans	agef-1	WBGENE00012386

Paralogs (15): CYTH3 (ENSG00000008256), PSD (ENSG00000059915), MON2 (ENSG00000061987), ARFGEF1 (ENSG00000066777), CYTH4 (ENSG00000100055), CYTH2 (ENSG00000105443), GBF1 (ENSG00000107862), CYTH1 (ENSG00000108669), IQSEC3 (ENSG00000120645), ARFGEF2 (ENSG00000124198), IQSEC2 (ENSG00000124313), PSD4 (ENSG00000125637), IQSEC1 (ENSG00000144711), PSD2 (ENSG00000146005), FBXO8 (ENSG00000164117)

Protein

Protein identifiers

PH and SEC7 domain-containing protein 3 — Q9NYI0 (reviewed: Q9NYI0)

Alternative names: Epididymis tissue protein Li 20mP, Exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 D, Hepatocellular carcinoma-associated antigen 67, Pleckstrin homology and SEC7 domain-containing protein 3

All UniProt accessions (9): Q9NYI0, B4DKF8, E5RFG7, E5RH02, E5RIH3, E5RJ29, E5RJE4, H0YAQ7, H0YC20

UniProt curated annotations — full annotation on UniProt →

Function. Guanine nucleotide exchange factor for ARF6.

Subcellular location. Cell membrane. Cell projection. Ruffle membrane. Postsynaptic density.

Tissue specificity. Isoform 2 is expressed in epididymis (at protein level).

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NYI0-1	1	yes
Q9NYI0-2	2
Q9NYI0-3	3

RefSeq proteins (28): NP_001349748, NP_001399794, NP_001399795, NP_001399799, NP_001399800, NP_001399801, NP_001399802, NP_001399803, NP_001399804, NP_001399805, NP_001399809, NP_001399811, NP_001399812, NP_001399813, NP_001399814, NP_001399815, NP_001399816, NP_001399817, NP_001399818, NP_001399819, NP_001399820, NP_001399821, NP_001399822, NP_001399823, NP_001399824, NP_001399825, NP_056125, NP_996792 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000904	Sec7_dom	Domain
IPR001849	PH_domain	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR023394	Sec7_C_sf	Homologous_superfamily
IPR035999	Sec7_dom_sf	Homologous_superfamily
IPR041681	PH_9	Domain

Pfam: PF01369, PF15410

UniProt features (30 total): modified residue 7, region of interest 7, compositionally biased region 6, splice variant 3, sequence variant 3, domain 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYI0-F1	55.73	0.19

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 (7): 76, 770, 1009, 1011, 1012, 1014, 1020

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 366 (showing top): GCACCTT_MIR18A_MIR18B, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, AREB6_03, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_RUFFLE, CHANDRAN_METASTASIS_DN, YGACNNYACAR_UNKNOWN, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, RIGGI_EWING_SARCOMA_PROGENITOR_DN, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, ACATTCC_MIR1_MIR206

GO Biological Process (1): regulation of ARF protein signal transduction (GO:0032012)

GO Molecular Function (3): guanyl-nucleotide exchange factor activity (GO:0005085), protein binding (GO:0005515), phospholipid binding (GO:0005543)

GO Cellular Component (6): postsynaptic density (GO:0014069), ruffle membrane (GO:0032587), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
ARF protein signal transduction	1
regulation of small GTPase mediated signal transduction	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
binding	1
lipid binding	1
asymmetric synapse	1
postsynaptic specialization	1
ruffle	1
cell projection membrane	1
leading edge membrane	1
membrane	1
cell periphery	1
cell junction	1

Protein interactions and networks

STRING

744 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PSD3	ARF6	P26438	594
PSD3	TMEM161B	Q8NDZ6	525
PSD3	PIGG	Q5H8A4	476
PSD3	FNDC3A	Q9Y2H6	414
PSD3	POFUT3	Q6P4F1	393
PSD3	DCUN1D4	Q92564	391
PSD3	TPST1	O60507	387
PSD3	SH2D4A	Q9H788	375
PSD3	CHRNA6	Q15825	355
PSD3	VPS13A	Q96RL7	352
PSD3	F8WDG0	F8WDG0	351
PSD3	ETDA	Q3ZM63	348
PSD3	TMCO4	Q5TGY1	347
PSD3	RIMKLA	Q8IXN7	345
PSD3	RABIF	P47224	339

IntAct

50 interactions, top by confidence:

A	B	Type	Score
YWHAG	BLTP3B	psi-mi:“MI:2364”(proximity)	0.640
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAH	BLTP3B	psi-mi:“MI:2364”(proximity)	0.570
YWHAG	SHTN1	psi-mi:“MI:0914”(association)	0.560
YWHAB	SHTN1	psi-mi:“MI:0914”(association)	0.530
YWHAE	SHTN1	psi-mi:“MI:0914”(association)	0.530
YWHAZ	SHTN1	psi-mi:“MI:0914”(association)	0.530
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
PB2	HAX1	psi-mi:“MI:0914”(association)	0.350
PB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB2	IPO5	psi-mi:“MI:0914”(association)	0.350
APP	ESYT2	psi-mi:“MI:0914”(association)	0.350
YWHAH	SHTN1	psi-mi:“MI:0914”(association)	0.350
YWHAQ	SHTN1	psi-mi:“MI:0914”(association)	0.350
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
COPA	ESYT2	psi-mi:“MI:0914”(association)	0.350
COPB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
YWHAH	FOXO6	psi-mi:“MI:0914”(association)	0.350
NPAS1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
EEF1AKMT3	SMCHD1	psi-mi:“MI:0914”(association)	0.350
CREB3L2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CTDSPL	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
PTPRA	EXOC3	psi-mi:“MI:2364”(proximity)	0.270
PTPRG	HSPA12A	psi-mi:“MI:2364”(proximity)	0.270
FGFR4	SH3PXD2B	psi-mi:“MI:2364”(proximity)	0.270
YWHAH	E2F8	psi-mi:“MI:2364”(proximity)	0.270
SFN	BLTP3B	psi-mi:“MI:2364”(proximity)	0.270
YWHAG	E2F8	psi-mi:“MI:2364”(proximity)	0.270
PSD3	trpB	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (82): PSD3 (Two-hybrid), PSD3 (Synthetic Growth Defect), PSD3 (Proximity Label-MS), PSD3 (Proximity Label-MS), PSD3 (Proximity Label-MS), PSD3 (Proximity Label-MS), PSD3 (Affinity Capture-RNA), PSD3 (Proximity Label-MS), PSD3 (Affinity Capture-MS), PSD3 (Affinity Capture-MS), PSD3 (Affinity Capture-MS), PSD3 (Affinity Capture-MS), PSD3 (Proximity Label-MS), PSD3 (Proximity Label-MS), PSD3 (Proximity Label-MS)

ESM2 similar proteins: A0FKI7, A2AHC3, A2AIW0, A4IH95, A5WUN7, A5WV69, A6H5Y1, A8MW92, D3Z8E6, P07106, P28290, P59598, Q08AD1, Q12912, Q2PFD7, Q3KQW7, Q4KLH6, Q4V9H5, Q502L1, Q52KN3, Q5R7V3, Q5REF4, Q5RHB5, Q5RJ80, Q5T5Y3, Q5T8D3, Q5XG73, Q5XI67, Q5ZHQ6, Q60664, Q640L3, Q640U0, Q641E3, Q6IRN6, Q6NPP4, Q6NRK3, Q6ZVD7, Q70EL1, Q76N89, Q8IX21

Diamond homologs: A0A0G2JUG7, A2A5R2, A5PKW4, D4A631, E1JIT7, F1MUS9, F4IXW2, F4JN05, F4JSZ5, F4K2K3, G3X9K3, G5EET6, O08967, O13690, O13817, O43739, O46382, P11075, P34512, P39993, P47102, P63034, P63035, P97694, P97696, Q10491, Q15438, Q2KI41, Q2PFD7, Q3TES0, Q42510, Q54KA7, Q5DTT2, Q5DU25, Q5E9G6, Q5JU85, Q6DFZ1, Q6DN90, Q6P1I6, Q76M68

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of BAD and translocation to mitochondria	7	231.7×	3e-14
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	204.4×	5e-14
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	204.4×	5e-14
Activation of BH3-only proteins	7	151.1×	5e-13
RHO GTPases activate PKNs	7	96.5×	1e-11
Intrinsic Pathway for Apoptosis	7	89.1×	2e-11
FOXO-mediated transcription	5	73.0×	6e-08
Translocation of SLC2A4 (GLUT4) to the plasma membrane	8	53.7×	2e-11

GO biological processes:

GO term	Partners	Fold	FDR
protein targeting	5	59.1×	3e-06
intracellular protein localization	7	23.6×	3e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	104
Likely benign	8
Benign	10

Top pathogenic / likely-pathogenic (0)

SpliceAI

4757 predictions. Top by Δscore:

Variant	Effect	Δscore
8:18535724:T:TA	donor_gain	1.0000
8:18535790:T:TA	donor_gain	1.0000
8:18556204:CACA:C	donor_loss	1.0000
8:18556205:ACAC:A	donor_loss	1.0000
8:18556246:T:C	donor_gain	1.0000
8:18556261:TTG:T	donor_gain	1.0000
8:18556350:CTC:C	acceptor_gain	1.0000
8:18556352:CCTG:C	acceptor_loss	1.0000
8:18556353:C:CA	acceptor_loss	1.0000
8:18556353:C:CC	acceptor_gain	1.0000
8:18556354:T:C	acceptor_loss	1.0000
8:18556375:T:C	acceptor_gain	1.0000
8:18556375:T:TC	acceptor_gain	1.0000
8:18572522:GATTA:G	donor_loss	1.0000
8:18572523:ATTAC:A	donor_loss	1.0000
8:18572524:TTAC:T	donor_loss	1.0000
8:18572525:TA:T	donor_loss	1.0000
8:18572526:A:AT	donor_loss	1.0000
8:18572527:CCT:C	donor_loss	1.0000
8:18575126:A:AC	donor_gain	1.0000
8:18575127:C:CT	donor_gain	1.0000
8:18575127:CT:C	donor_gain	1.0000
8:18575127:CTG:C	donor_gain	1.0000
8:18575127:CTGA:C	donor_gain	1.0000
8:18575127:CTGAG:C	donor_gain	1.0000
8:18575131:G:C	donor_gain	1.0000
8:18575150:T:A	donor_gain	1.0000
8:18575189:T:TA	donor_gain	1.0000
8:18575281:TCATC:T	acceptor_gain	1.0000
8:18575282:CATC:C	acceptor_gain	1.0000

AlphaMissense

6901 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:18556219:A:G	L974P	1.000
8:18572650:A:G	W889R	1.000
8:18572650:A:T	W889R	1.000
8:18575140:A:G	L877P	1.000
8:18575167:A:G	L868P	1.000
8:18575167:A:T	L868H	1.000
8:18600377:A:G	L824P	1.000
8:18600392:A:G	L819P	1.000
8:18600412:C:A	W812C	1.000
8:18600412:C:G	W812C	1.000
8:18600413:C:G	W812S	1.000
8:18600414:A:G	W812R	1.000
8:18600414:A:T	W812R	1.000
8:18632641:T:A	K795N	1.000
8:18632641:T:G	K795N	1.000
8:18632642:T:A	K795I	1.000
8:18632643:T:C	K795E	1.000
8:18804582:A:T	V617D	1.000
8:18535854:A:C	S1012R	0.999
8:18535854:A:T	S1012R	0.999
8:18535856:T:G	S1012R	0.999
8:18535951:C:G	R980P	0.999
8:18535952:G:T	R980S	0.999
8:18572556:A:G	L920P	0.999
8:18572566:G:T	R917S	0.999
8:18572570:A:C	F915L	0.999
8:18572570:A:T	F915L	0.999
8:18572571:A:G	F915S	0.999
8:18572572:A:G	F915L	0.999
8:18572613:G:A	S901F	0.999

dbSNP variants (sampled 300 via entrez): RS1000004579 (8:18819549 T>C), RS1000009809 (8:18864800 C>A,T), RS1000015489 (8:18599868 T>C), RS1000019441 (8:18619398 A>C), RS1000024662 (8:18627239 T>A), RS1000026095 (8:18949785 C>A), RS1000028077 (8:18772099 A>G), RS1000028846 (8:18799862 C>T), RS1000034025 (8:18591226 C>T), RS1000047547 (8:18571423 A>G), RS1000048010 (8:18889705 T>G), RS1000049384 (8:19001183 C>T), RS1000056882 (8:18645288 G>C), RS1000064554 (8:18588110 C>G,T), RS1000065370 (8:18932494 A>T)

Disease associations

OMIM: gene MIM:614440 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
antecubital pterygium syndrome	Limited	Unknown

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
antecubital pterygium syndrome	Limited	AD

Mondo (1): antecubital pterygium syndrome (MONDO:0008339)

Orphanet (0):

HPO phenotypes

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

GWAS associations

48 associations (top):

Study	Trait	p-value
GCST001059_20	Neutrophil count	4.000000e-06
GCST001762_376	Obesity-related traits	5.000000e-06
GCST002074_8	Paclitaxel-induced neuropathy	4.000000e-06
GCST002382_2	Urinary albumin excretion rate in type 1 diabetes	4.000000e-06
GCST002829_26	Urate levels in overweight individuals	1.000000e-06
GCST003075_131	Cognitive decline rate in late mild cognitive impairment	8.000000e-07
GCST003075_30	Cognitive decline rate in late mild cognitive impairment	5.000000e-06
GCST003448_6	Erythrocyte cadmium concentration in never smokers	8.000000e-06
GCST003632_3	Survival in sporadic amyotrophic lateral sclerosis	3.000000e-07
GCST004101_2	Body mass index (change over time) in gastrointestinal cancer	7.000000e-06
GCST004350_6	Bone ultrasound measurement (velocity of sound)	4.000000e-07
GCST005175_63	Coronary artery calcified atherosclerotic plaque (90 or 130 HU threshold) in type 2 diabetes	5.000000e-06
GCST006003_15	Triglyceride levels	1.000000e-08
GCST007201_357	Schizophrenia	9.000000e-06
GCST007201_94	Schizophrenia	1.000000e-08
GCST008074_111	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	3.000000e-16
GCST008074_40	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2.000000e-28
GCST008074_5	Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	2.000000e-11
GCST008076_2	Triglyceride levels	5.000000e-09
GCST008076_29	Triglyceride levels	7.000000e-15
GCST008076_67	Triglyceride levels	2.000000e-07
GCST008078_141	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	3.000000e-07
GCST008078_43	LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	8.000000e-07
GCST008079_130	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	3.000000e-08
GCST008079_70	LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	9.000000e-08
GCST008083_157	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	1.000000e-16
GCST008083_71	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	8.000000e-12
GCST008083_79	Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	3.000000e-29
GCST008087_109	Triglyceride levels in current drinkers	4.000000e-09
GCST008087_49	Triglyceride levels in current drinkers	1.000000e-10

EFO canonical traits (17, from GWAS)

EFO ID	Trait name
EFO:0004833	neutrophil count
EFO:0005667	urinary albumin excretion rate
EFO:0004531	urate measurement
EFO:0007710	cognitive decline measurement
EFO:0000714	survival time
EFO:0005937	longitudinal BMI measurement
EFO:0004514	bone quantitative ultrasound measurement
EFO:0004723	coronary artery calcification
EFO:0004530	triglyceride measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004329	alcohol drinking
EFO:0004468	glucose measurement
EFO:0005420	grey matter volume measurement
EFO:0010553	cocaine use measurement
EFO:0004574	total cholesterol measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0009270	heel bone mineral density

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566738	Pterygium, Antecubital (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	6
Tetrachlorodibenzodioxin	decreases expression, increases expression	3
Tobacco Smoke Pollution	decreases expression, decreases methylation, increases expression	3
trichostatin A	affects expression, increases expression	2
sodium arsenite	decreases expression, increases abundance	2
Acetaminophen	increases expression	2
Arsenic	affects methylation, decreases expression, increases abundance	2
Estradiol	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
Valproic Acid	affects cotreatment, increases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
sotorasib	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
2,4,5,2’,4’,5’-hexachlorobiphenyl	increases expression	1
arsenite	affects binding, decreases reaction	1
coenzyme Q10	decreases reaction, increases expression	1
aflatoxin B2	decreases methylation	1
nickel sulfate	decreases expression	1
tacedinaline	increases expression	1
CGP 52608	affects binding, increases reaction	1
oxamflatin	increases expression	1
apicidin	increases expression	1
scriptaid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1

Clinical trials (associated diseases)

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