SCMH1

Summary

SCMH1 (Scm polycomb group protein homolog 1, HGNC:19003) is a protein-coding gene on chromosome 1p34.2, encoding Polycomb protein SCMH1 (Q96GD3). Associates with Polycomb group (PcG) multiprotein complexes; the complex class is required to maintain the transcriptionally repressive state of some genes.

Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in heterochromatin formation and negative regulation of DNA-templated transcription. Predicted to act upstream of or within anterior/posterior pattern specification; chromatin remodeling; and spermatogenesis. Predicted to be located in nucleoplasm. Predicted to be active in nucleus.

Source: NCBI Gene 22955 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 91 total
• MANE Select transcript: NM_001394311

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19003
Approved symbol	SCMH1
Name	Scm polycomb group protein homolog 1
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	Scml3
Ensembl gene	ENSG00000010803
Ensembl biotype	protein_coding
OMIM	616396
Entrez	22955

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 19 protein_coding, 4 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000326197, ENST00000337495, ENST00000372595, ENST00000372596, ENST00000372597, ENST00000456518, ENST00000460215, ENST00000472037, ENST00000482530, ENST00000488592, ENST00000489421, ENST00000498793, ENST00000695335, ENST00000695336, ENST00000695337, ENST00000850937, ENST00000850938, ENST00000906276, ENST00000906277, ENST00000906278, ENST00000936334, ENST00000949693, ENST00000949694, ENST00000949695, ENST00000949696, ENST00000949697

RefSeq mRNA: 21 — MANE Select: NM_001394311 NM_001031694, NM_001172218, NM_001172219, NM_001172220, NM_001172221, NM_001172222, NM_001350667, NM_001350668, NM_001394299, NM_001394300, NM_001394301, NM_001394302, NM_001394303, NM_001394304, NM_001394305, NM_001394306, NM_001394307, NM_001394308, NM_001394309, NM_001394311, NM_012236

CCDS: CCDS30688, CCDS461, CCDS53301, CCDS53302, CCDS53303, CCDS53304, CCDS90927, CCDS90928

Canonical transcript exons

ENST00000695335 — 16 exons

Exon	Start	End
ENSE00000768679	41070595	41070721
ENSE00000768714	41075219	41075451
ENSE00000768876	41113283	41113526
ENSE00000870127	41116922	41117010
ENSE00001190678	41027202	41028319
ENSE00003469342	41037362	41037541
ENSE00003475050	41161364	41161432
ENSE00003503603	41160875	41160898
ENSE00003515629	41028584	41028726
ENSE00003526466	41151614	41151684
ENSE00003561389	41048690	41048890
ENSE00003619263	41046407	41046598
ENSE00003628096	41186121	41186250
ENSE00003690326	41033983	41034048
ENSE00003693990	41142878	41143112
ENSE00003963459	41242059	41242306

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 95.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.8739 / max 158.4234, expressed in 1738 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11945	5.6679	1559
11949	2.5579	1284
11947	2.2350	1141
11948	0.2512	78
11946	0.1619	53

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus muscularis layer	UBERON:0035833	95.66	gold quality
lower esophagus	UBERON:0013473	95.63	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.58	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.29	gold quality
popliteal artery	UBERON:0002250	95.08	gold quality
tibial artery	UBERON:0007610	95.07	gold quality
body of uterus	UBERON:0009853	95.00	gold quality
mucosa of stomach	UBERON:0001199	94.98	gold quality
aorta	UBERON:0000947	94.70	gold quality
thoracic aorta	UBERON:0001515	94.37	gold quality
ascending aorta	UBERON:0001496	94.36	gold quality
descending thoracic aorta	UBERON:0002345	94.07	gold quality
right coronary artery	UBERON:0001625	94.06	gold quality
left uterine tube	UBERON:0001303	94.05	gold quality
left ovary	UBERON:0002119	93.91	gold quality
body of pancreas	UBERON:0001150	93.88	gold quality
right ovary	UBERON:0002118	93.68	gold quality
right testis	UBERON:0004534	93.57	gold quality
left testis	UBERON:0004533	93.49	gold quality
left coronary artery	UBERON:0001626	93.16	gold quality
right atrium auricular region	UBERON:0006631	93.04	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.89	gold quality
endocervix	UBERON:0000458	92.66	gold quality
coronary artery	UBERON:0001621	92.49	gold quality
apex of heart	UBERON:0002098	92.34	gold quality
cardiac atrium	UBERON:0002081	92.28	gold quality
body of stomach	UBERON:0001161	92.26	gold quality
muscle of leg	UBERON:0001383	92.23	gold quality
gastrocnemius	UBERON:0001388	92.19	gold quality
metanephros cortex	UBERON:0010533	91.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.48

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HOXA9

miRNA regulators (miRDB)

46 targeting SCMH1, 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-4533	100.00	69.48	2758
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-6838-3P	98.40	65.88	559
HSA-MIR-4299	98.28	66.96	850
HSA-MIR-6867-3P	98.12	66.07	1305
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-3909	97.55	66.78	887

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	scmh1	ENSDARG00000104311
mus_musculus	Scmh1	ENSMUSG00000000085
rattus_norvegicus	Scmh1	ENSRNOG00000071308
drosophila_melanogaster	l(3)mbt	FBGN0002441
drosophila_melanogaster	Sfmbt	FBGN0032475
caenorhabditis_elegans	lin-61	WBGENE00003041
caenorhabditis_elegans	mbtr-1	WBGENE00021661

Paralogs (18): MBTD1 (ENSG00000011258), SCML1 (ENSG00000047634), L3MBTL2 (ENSG00000100395), SCML2 (ENSG00000102098), PHC1 (ENSG00000111752), THAP10 (ENSG00000129028), PHC2 (ENSG00000134686), SAMD1 (ENSG00000141858), SCML4 (ENSG00000146285), L3MBTL4 (ENSG00000154655), SFMBT1 (ENSG00000163935), PHC3 (ENSG00000173889), L3MBTL1 (ENSG00000185513), SAMD7 (ENSG00000187033), SAMD11 (ENSG00000187634), SFMBT2 (ENSG00000198879), L3MBTL3 (ENSG00000198945), SAMD13 (ENSG00000203943)

Protein

Protein identifiers

Polycomb protein SCMH1 — Q96GD3 (reviewed: Q96GD3)

Alternative names: Sex comb on midleg homolog 1

All UniProt accessions (5): Q96GD3, A0A087WW29, A0A8Q3SHN2, A0A8Q3SHR9, B4DWE6

UniProt curated annotations — full annotation on UniProt →

Function. Associates with Polycomb group (PcG) multiprotein complexes; the complex class is required to maintain the transcriptionally repressive state of some genes.

Subunit / interactions. Interacts with the SAM domain of PHC1 via its SAM domain in vitro. Associates with a PRC1-like complex.

Subcellular location. Nucleus.

Tissue specificity. Strongly expressed in heart, muscle and pancreas. Weakly expressed in brain, placenta, lung, liver and kidney.

Miscellaneous. May be due to intron retention.

Similarity. Belongs to the SCM family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q96GD3-1	1	yes
Q96GD3-2	2
Q96GD3-3	3
Q96GD3-4	4
Q96GD3-5	5
Q96GD3-6	6

RefSeq proteins (21): NP_001026864, NP_001165689, NP_001165690, NP_001165691, NP_001165692, NP_001165693, NP_001337596, NP_001337597, NP_001381228, NP_001381229, NP_001381230, NP_001381231, NP_001381232, NP_001381233, NP_001381234, NP_001381235, NP_001381236, NP_001381237, NP_001381238, NP_001381240, NP_036368 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001660	SAM	Domain
IPR004092	Mbt	Domain
IPR013761	SAM/pointed_sf	Homologous_superfamily
IPR021987	SLED	Domain
IPR033763	SCML2_RBR	Domain
IPR038348	SLED_sf	Homologous_superfamily
IPR047279	MBT_SCMH1_rpt1	Repeat
IPR047280	MBT_SCMH1_rpt2	Repeat
IPR047531	SAM_Scm-like	Domain
IPR050548	PcG_chromatin_remod_factors	Family

Pfam: PF00536, PF02820, PF12140, PF17208

UniProt features (31 total): strand 9, helix 7, splice variant 5, compositionally biased region 3, repeat 2, chain 1, sequence conflict 1, turn 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2P0K	X-RAY DIFFRACTION	1.75

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96GD3-F1	71.39	0.49

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-2559580	Oxidative Stress Induced Senescence
R-HSA-3108214	SUMOylation of DNA damage response and repair proteins
R-HSA-3899300	SUMOylation of transcription cofactors
R-HSA-4551638	SUMOylation of chromatin organization proteins
R-HSA-4570464	SUMOylation of RNA binding proteins
R-HSA-4655427	SUMOylation of DNA methylation proteins
R-HSA-8939243	RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8943724	Regulation of PTEN gene transcription
R-HSA-9976102	Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)

MSigDB gene sets: 143 (showing top): RORA1_01, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, MARTINEZ_RB1_TARGETS_DN, chr1p34, PARK_HSC_AND_MULTIPOTENT_PROGENITORS, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, AGTCAGC_MIR345, GOBP_CHROMATIN_REMODELING, GOBP_HETEROCHROMATIN_ORGANIZATION, GOBP_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_CHROMATIN_BINDING, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_HISTONE_BINDING

GO Biological Process (6): heterochromatin formation (GO:0031507), negative regulation of DNA-templated transcription (GO:0045892), chromatin remodeling (GO:0006338), regulation of DNA-templated transcription (GO:0006355), spermatogenesis (GO:0007283), anterior/posterior pattern specification (GO:0009952)

GO Molecular Function (3): chromatin binding (GO:0003682), histone binding (GO:0042393), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), male germ cell nucleus (GO:0001673), chromocenter (GO:0010369)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
SUMO E3 ligases SUMOylate target proteins	5
Cellular Senescence	1
Transcriptional regulation by RUNX1	1
PTEN Regulation	1
Differentiation of T cells	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	2
binding	2
cellular component assembly	1
heterochromatin boundary formation	1
negative regulation of gene expression, epigenetic	1
heterochromatin organization	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
chromatin organization	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
developmental process involved in reproduction	1
male gamete generation	1
regionalization	1
protein binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
germ cell nucleus	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

873 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCMH1	PCGF2	P35227	937
SCMH1	BMI1	P35226	926
SCMH1	R4GMX3	R4GMX3	926
SCMH1	CBX2	Q14781	742
SCMH1	RING1	Q06587	733
SCMH1	RNF2	Q99496	692
SCMH1	MSMB	P08118	671
SCMH1	TTK	P33981	651
SCMH1	PHC1	P78364	648
SCMH1	CBX6	O95503	594
SCMH1	CBX8	Q9HC52	553
SCMH1	CBX7	O95931	526
SCMH1	CBX4	O00257	521
SCMH1	PCGF1	Q9BSM1	480
SCMH1	EIF2B3	Q9NR50	478

IntAct

49 interactions, top by confidence:

A	B	Type	Score
BMI1	CBX4	psi-mi:“MI:0914”(association)	0.900
PCGF2	CBX4	psi-mi:“MI:0914”(association)	0.840
PHC1	CBX4	psi-mi:“MI:0914”(association)	0.790
RING1	CBX4	psi-mi:“MI:0914”(association)	0.730
CBX8	CBX4	psi-mi:“MI:0914”(association)	0.670
SCMH1	MAGEA12	psi-mi:“MI:0915”(physical association)	0.560
SCMH1	UBQLN1	psi-mi:“MI:0915”(physical association)	0.560
UBQLN1	SCMH1	psi-mi:“MI:0915”(physical association)	0.560
SCMH1	SFMBT1	psi-mi:“MI:0915”(physical association)	0.560
SFMBT2	SCMH1	psi-mi:“MI:0915”(physical association)	0.560
SCMH1	HPCAL4	psi-mi:“MI:0915”(physical association)	0.560
	SCMH1	psi-mi:“MI:0915”(physical association)	0.370
SCMH1	FXR1	psi-mi:“MI:0915”(physical association)	0.370
SCMH1	FXR2	psi-mi:“MI:0915”(physical association)	0.370
SCMH1	TSC1	psi-mi:“MI:0915”(physical association)	0.370
EWSR1	SCMH1	psi-mi:“MI:0915”(physical association)	0.370
PCBD1	SCMH1	psi-mi:“MI:0915”(physical association)	0.370
LZTR1	SCMH1	psi-mi:“MI:0915”(physical association)	0.370
SCMH1	MAML3	psi-mi:“MI:0915”(physical association)	0.370
SCMH1	CBX4	psi-mi:“MI:0914”(association)	0.350
Bmi1	CBX4	psi-mi:“MI:0914”(association)	0.350
Cbx2	CBX4	psi-mi:“MI:0914”(association)	0.350

BioGRID (75): SCMH1 (Two-hybrid), UBQLN1 (Two-hybrid), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), SCMH1 (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), PGK2 (Affinity Capture-MS), GNB2 (Affinity Capture-MS)

ESM2 similar proteins: A0JNA8, A2AFR3, A2AWP8, F1LXF1, O15034, O94844, O94967, O95267, P11274, P28028, Q01826, Q08BT5, Q14161, Q14CM0, Q15139, Q3UGM2, Q3UHE1, Q4R4I0, Q5R5M3, Q5VUG0, Q5XIS9, Q60611, Q62101, Q66H91, Q68FF6, Q6NZQ4, Q6PAJ1, Q6PB44, Q6ZW49, Q6ZWH5, Q80U28, Q8BWW9, Q8BZ03, Q8CGF6, Q8TCU6, Q8VDD9, Q8VI24, Q96GD3, Q9BZ71, Q9BZL6

Diamond homologs: A2A5N8, B1B1A0, D3YUG0, D3YXK1, D3ZWK4, E1C2V1, O02274, O60284, O95251, P39769, P59178, P70047, P70475, P78364, P97500, Q01538, Q05BQ5, Q1JQD9, Q1RNF8, Q29L50, Q32N90, Q3MIF2, Q4V7W5, Q5DTW2, Q5R737, Q5SVQ0, Q5VUG0, Q5VXD3, Q64028, Q6DIN3, Q6P5G3, Q6SPE9, Q6SPF0, Q7Z3H4, Q80TY4, Q810T5, Q8BLB7, Q8C8Y5, Q8CFC2, Q8CHP6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 31 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
SUMOylation of DNA methylation proteins	7	276.6×	5e-15
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known	7	123.8×	2e-12
SUMOylation of transcription cofactors	7	100.0×	4e-12
SUMOylation of RNA binding proteins	7	98.0×	4e-12
Regulation of PTEN gene transcription	7	73.5×	3e-11
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)	8	68.9×	2e-12
SUMOylation of chromatin organization proteins	7	65.3×	6e-11
SUMOylation of DNA damage response and repair proteins	7	60.3×	9e-11

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2063 predictions. Top by Δscore:

Variant	Effect	Δscore
1:41028582:A:AC	donor_gain	1.0000
1:41028583:C:CC	donor_gain	1.0000
1:41037360:ACC:A	donor_gain	1.0000
1:41037361:CCC:C	donor_gain	1.0000
1:41046594:CACGG:C	acceptor_gain	1.0000
1:41046596:CGG:C	acceptor_gain	1.0000
1:41046599:C:CC	acceptor_gain	1.0000
1:41048887:CAAA:C	acceptor_gain	1.0000
1:41048889:AA:A	acceptor_gain	1.0000
1:41048891:C:CC	acceptor_gain	1.0000
1:41070589:TCTTA:T	donor_loss	1.0000
1:41070590:CTTA:C	donor_loss	1.0000
1:41070591:TTAC:T	donor_loss	1.0000
1:41070592:TA:T	donor_loss	1.0000
1:41070593:A:AG	donor_loss	1.0000
1:41070717:TTCCT:T	acceptor_gain	1.0000
1:41070718:TCCT:T	acceptor_gain	1.0000
1:41070719:CCTC:C	acceptor_gain	1.0000
1:41070720:CT:C	acceptor_gain	1.0000
1:41070721:TC:T	acceptor_loss	1.0000
1:41070722:C:CC	acceptor_gain	1.0000
1:41070722:CTGTC:C	acceptor_loss	1.0000
1:41070723:T:A	acceptor_loss	1.0000
1:41070726:C:CT	acceptor_gain	1.0000
1:41142872:A:AC	donor_gain	1.0000
1:41142872:ACT:A	donor_gain	1.0000
1:41142873:C:CT	donor_gain	1.0000
1:41142873:CT:C	donor_gain	1.0000
1:41142873:CTC:C	donor_gain	1.0000
1:41142873:CTCA:C	donor_gain	1.0000

AlphaMissense

4390 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:41028240:A:G	L646P	1.000
1:41028258:A:G	L640P	1.000
1:41028291:A:G	L629P	1.000
1:41028300:A:G	L626P	1.000
1:41028309:C:T	G623D	1.000
1:41028315:A:C	I621S	1.000
1:41028594:A:G	F616S	1.000
1:41048773:A:T	V398D	1.000
1:41048809:C:T	G386E	1.000
1:41113323:A:C	C225W	1.000
1:41113324:C:T	C225Y	1.000
1:41113325:A:G	C225R	1.000
1:41113328:A:G	W224R	1.000
1:41113328:A:T	W224R	1.000
1:41113372:T:A	D209V	1.000
1:41113374:A:C	F208L	1.000
1:41113374:A:T	F208L	1.000
1:41113375:A:C	F208C	1.000
1:41113375:A:G	F208S	1.000
1:41113376:A:C	F208V	1.000
1:41113376:A:G	F208L	1.000
1:41113376:A:T	F208I	1.000
1:41113378:G:T	A207D	1.000
1:41113386:C:A	W204C	1.000
1:41113386:C:G	W204C	1.000
1:41113387:C:G	W204S	1.000
1:41113388:A:G	W204R	1.000
1:41113388:A:T	W204R	1.000
1:41113390:C:A	G203V	1.000
1:41113390:C:T	G203E	1.000

dbSNP variants (sampled 300 via entrez): RS1000005548 (1:41129368 C>T), RS1000017210 (1:41123215 C>A,G), RS1000037567 (1:41085135 TAAATA>T,TAAATAAAATA), RS1000044786 (1:41130808 G>T), RS1000048207 (1:41039760 A>C), RS1000068362 (1:41161850 T>C), RS1000095058 (1:41080915 A>G,T), RS1000098389 (1:41129725 C>T), RS1000098927 (1:41176651 T>A), RS1000107702 (1:41191613 T>C), RS1000123488 (1:41174967 T>C), RS1000129624 (1:41215454 T>A,C), RS1000153894 (1:41229763 G>C), RS1000171195 (1:41033605 G>T), RS1000176776 (1:41196939 T>G)

Disease associations

OMIM: gene MIM:616396 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST000174_10	Height	2.000000e-08
GCST000817_91	Height	2.000000e-12
GCST001956_40	Height	3.000000e-09
GCST002647_84	Height	2.000000e-20
GCST004364_29	Intelligence	4.000000e-09
GCST004364_9	Intelligence	1.000000e-08
GCST005316_275	Intelligence (MTAG)	4.000000e-08
GCST006061_177	Atrial fibrillation	2.000000e-07
GCST006414_102	Atrial fibrillation	3.000000e-10
GCST007324_20	Adventurousness	2.000000e-09
GCST007325_192	General risk tolerance (MTAG)	2.000000e-08
GCST011771_2	Rapid response to perioperative phenylephrine (change in mean arterial pressure)	6.000000e-08
GCST012227_1396	Hip circumference adjusted for BMI	4.000000e-11
GCST90000025_918	Appendicular lean mass	6.000000e-18
GCST90000025_919	Appendicular lean mass	9.000000e-60
GCST90000026_1	Appendicular lean mass	4.000000e-06
GCST90000027_26	Appendicular lean mass	1.000000e-13

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0008579	risk-taking behaviour
EFO:0006943	blood pressure change measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Cyclosporine	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	decreases expression, affects cotreatment	1
bisphenol A	increases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
periodate-oxidized adenosine	affects expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
perfluoro-n-nonanoic acid	increases expression	1
abrine	increases expression	1
Air Pollutants	decreases expression	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Dexamethasone	affects cotreatment, decreases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methapyrilene	increases methylation	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases methylation	1
Vitamin E	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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