UMAD1

Summary

UMAD1 (UBAP1-MVB12-associated (UMA) domain containing 1, HGNC:48955) is a protein-coding gene on chromosome 7p21.3, encoding UBAP1-MVB12-associated (UMA)-domain containing protein 1 (C9J7I0).

At a glance

• GWAS associations: 21
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001302348

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48955
Approved symbol	UMAD1
Name	UBAP1-MVB12-associated (UMA) domain containing 1
Location	7p21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000219545
Ensembl biotype	protein_coding
Entrez	729852

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 3 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay

ENST00000406829, ENST00000463725, ENST00000471760, ENST00000482067, ENST00000493246, ENST00000636849, ENST00000638342, ENST00000639110, ENST00000639343, ENST00000682710, ENST00000892838, ENST00000892839, ENST00000892840, ENST00000892841, ENST00000935492, ENST00000949979, ENST00000949980, ENST00000949981

RefSeq mRNA: 3 — MANE Select: NM_001302348 NM_001302348, NM_001302349, NM_001302350

CCDS: CCDS83158

Canonical transcript exons

ENST00000682710 — 4 exons

Exon	Start	End
ENSE00001925959	7640752	7640821
ENSE00003794769	7801670	7801743
ENSE00003799907	7673309	7673453
ENSE00003917777	7877281	7879223

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 91.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.3841 / max 154.2692, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77202	16.3841	1803

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	91.46	gold quality
calcaneal tendon	UBERON:0003701	90.98	gold quality
pancreas	UBERON:0001264	89.78	gold quality
adrenal tissue	UBERON:0018303	88.75	gold quality
secondary oocyte	CL:0000655	88.71	gold quality
body of stomach	UBERON:0001161	88.47	gold quality
islet of Langerhans	UBERON:0000006	88.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.82	gold quality
left adrenal gland	UBERON:0001234	87.34	gold quality
right adrenal gland cortex	UBERON:0035827	87.16	gold quality
popliteal artery	UBERON:0002250	87.08	gold quality
tibial artery	UBERON:0007610	87.07	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.97	gold quality
bone marrow cell	CL:0002092	86.87	gold quality
stomach	UBERON:0000945	86.77	gold quality
right adrenal gland	UBERON:0001233	86.64	gold quality
adrenal gland	UBERON:0002369	86.60	gold quality
left adrenal gland cortex	UBERON:0035825	86.51	gold quality
muscle of leg	UBERON:0001383	86.43	gold quality
gastrocnemius	UBERON:0001388	86.42	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.15	gold quality
aorta	UBERON:0000947	86.11	gold quality
hypothalamus	UBERON:0001898	85.88	gold quality
descending thoracic aorta	UBERON:0002345	85.66	gold quality
left lobe of thyroid gland	UBERON:0001120	85.65	gold quality
rectum	UBERON:0001052	85.64	gold quality
jejunal mucosa	UBERON:0000399	85.58	gold quality
gall bladder	UBERON:0002110	85.41	gold quality
adenohypophysis	UBERON:0002196	85.37	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.01
E-MTAB-6058	no	69.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

131 targeting UMAD1, 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-3064-3P	100.00	70.09	1254
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502

Literature-anchored findings (GeneRIF, showing 1)

• Association of the RPA3-UMAD1 locus with interstitial lung diseases complicated with rheumatoid arthritis in Japanese. (PMID:32737115)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	umad1	ENSDARG00000076008
mus_musculus	Umad1	ENSMUSG00000089862
rattus_norvegicus	Glcci1	ENSRNOG00000008524

Protein

Protein identifiers

UBAP1-MVB12-associated (UMA)-domain containing protein 1 — C9J7I0 (reviewed: C9J7I0)

Alternative names: RPA3 antisense RNA 1, RPA3 opposite strand

All UniProt accessions (5): C9J7I0, A0A1B0GUC2, A0A1B0GWD2, A0A1W2PNU7, A0A1W2PP33

RefSeq proteins (3): NP_001289277, NP_001289278, NP_001289279 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023340	UMA	Domain
IPR053292	UMAD1	Family

UniProt features (5 total): compositionally biased region 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9J7I0-F1	61.63	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GSE10240_IL22_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, BANP_TARGET_GENES, DIDO1_TARGET_GENES, DYRK1A_TARGET_GENES, ELF2_TARGET_GENES, NKX2_3_TARGET_GENES, RFX7_TARGET_GENES, UBN1_TARGET_GENES, ZNF213_TARGET_GENES, ZNF322_TARGET_GENES, ZNF561_TARGET_GENES, MIR513A_3P_MIR513C_3P, MIR3606_3P, MIR577

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

112 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UMAD1	GLCCI1	Q86VQ1	479
UMAD1	ANO2	Q9NQ90	417
UMAD1	NUP93	Q8N1F7	392
UMAD1	RPA3	P35244	358
UMAD1	EXOC6B	Q9Y2D4	290
UMAD1	OSBP2	Q969R2	252
UMAD1	CAMSAP1	Q5T5Y3	248
UMAD1	MAP3K7	O43318	227
UMAD1	NUP35	Q8NFH5	222
UMAD1	DCBLD2	Q96PD2	222
UMAD1	ERBB4	Q15303	182
UMAD1	PPP2R5A	Q15172	179
UMAD1	PTPRA	P18433	176
UMAD1	PSMA3	P25788	175
UMAD1	ASAP1	Q9ULH1	166

IntAct

20 interactions, top by confidence:

A	B	Type	Score
TSG101	VPS37C	psi-mi:“MI:0914”(association)	0.780
UMAD1	TH	psi-mi:“MI:0915”(physical association)	0.560
UMAD1	GABARAPL1	psi-mi:“MI:0915”(physical association)	0.560
Cep55	UMAD1	psi-mi:“MI:0914”(association)	0.350
TFG	NCOA4	psi-mi:“MI:0914”(association)	0.350
Ptpn23	UMAD1	psi-mi:“MI:0914”(association)	0.350
Vps28	UMAD1	psi-mi:“MI:0914”(association)	0.350
TRAF2	UMAD1	psi-mi:“MI:0914”(association)	0.350
BIRC2	UMAD1	psi-mi:“MI:0914”(association)	0.350
RBCK1	UMAD1	psi-mi:“MI:0914”(association)	0.350
TNIP1	UMAD1	psi-mi:“MI:0914”(association)	0.350
SHARPIN	UMAD1	psi-mi:“MI:0914”(association)	0.350
VPS37B	UMAD1	psi-mi:“MI:0914”(association)	0.350
SCN2B	RIMOC1	psi-mi:“MI:0914”(association)	0.350
TH	UMAD1	psi-mi:“MI:0915”(physical association)	0.000
GABARAPL1	UMAD1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-RNA), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS), UMAD1 (Two-hybrid), UMAD1 (Two-hybrid), UMAD1 (Affinity Capture-RNA), UMAD1 (Affinity Capture-MS), UMAD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUA6, A0A1B0GVH6, A0A2K1J5A5, A0A2K1JJ00, A0JM08, A0JM83, A2AWL7, A2BIL8, A4IGV6, C9J7I0, E9Q309, Q06616, Q09791, Q1RMQ5, Q3KP22, Q3T0A6, Q3URK1, Q3ZBP0, Q3ZBS1, Q498L0, Q4KMC9, Q4R309, Q4V7J0, Q5RD08, Q5VT06, Q6A065, Q6DFB0, Q6NWJ0, Q6P6I6, Q6PKN7, Q6ZPK7, Q703I1, Q758T8, Q80WR5, Q8BKK4, Q91XQ4, Q921K9, Q93ZL5, Q949U2, Q96GY3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 17 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.

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of canonical NF-kappaB signal transduction	5	61.4×	2e-06
positive regulation of canonical NF-kappaB signal transduction	5	25.9×	3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

704 predictions. Top by Δscore:

Variant	Effect	Δscore
7:7718513:A:AC	donor_gain	1.0000
7:7718514:C:CC	donor_gain	1.0000
7:7718514:CA:C	donor_gain	1.0000
7:7718514:CAA:C	donor_gain	1.0000
7:7718514:CAAA:C	donor_gain	1.0000
7:7718514:CAAAA:C	donor_gain	1.0000
7:7641175:CCTG:C	acceptor_loss	0.9900
7:7641176:C:A	acceptor_loss	0.9900
7:7641176:C:CC	acceptor_gain	0.9900
7:7641177:T:C	acceptor_loss	0.9900
7:7718509:ACTT:A	donor_loss	0.9900
7:7718510:CT:C	donor_loss	0.9900
7:7718511:TT:T	donor_loss	0.9900
7:7718512:TA:T	donor_loss	0.9900
7:7718513:A:AT	donor_loss	0.9900
7:7718514:C:CA	donor_loss	0.9900
7:7641172:CCAC:C	acceptor_gain	0.9800
7:7641173:CAC:C	acceptor_gain	0.9800
7:7641173:CACC:C	acceptor_gain	0.9800
7:7641512:C:CA	donor_gain	0.9700
7:7640756:TG:T	donor_gain	0.9500
7:7640970:C:A	donor_gain	0.9500
7:7641500:A:C	donor_gain	0.9500
7:7640944:CCAG:C	donor_gain	0.9400
7:7641171:TCCAC:T	acceptor_gain	0.9300
7:7641172:CCACC:C	acceptor_gain	0.9300
7:7718547:T:TA	donor_gain	0.9300
7:7640854:A:AC	donor_gain	0.9100
7:7640855:C:CC	donor_gain	0.9100
7:7641174:AC:A	acceptor_gain	0.9100

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000001233 (7:7806469 C>T), RS1000017584 (7:7766248 A>C), RS1000023489 (7:7812782 C>A,T), RS1000060916 (7:7669131 G>T), RS1000066519 (7:7742871 T>G), RS1000068166 (7:7775031 T>C), RS1000075239 (7:7809603 T>C), RS1000078765 (7:7668895 A>G), RS1000079546 (7:7738215 A>C), RS1000083508 (7:7853945 T>G), RS1000090822 (7:7852248 C>T), RS1000091289 (7:7650205 C>T), RS1000092092 (7:7783827 T>C), RS1000092788 (7:7796406 C>T), RS1000093680 (7:7814599 T>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST004613_154	Sum neutrophil eosinophil counts	4.000000e-09
GCST004614_98	Granulocyte count	3.000000e-09
GCST004624_108	Sum eosinophil basophil counts	2.000000e-09
GCST004746_16	Small cell lung carcinoma	2.000000e-06
GCST006134_4	Hippocampal volume	7.000000e-06
GCST007998_25	Intraocular pressure	4.000000e-07
GCST008156_117	Hip circumference adjusted for BMI	2.000000e-06
GCST008526_25	Coffee consumption	2.000000e-06
GCST009523_47	Household income	3.000000e-09
GCST009524_248	Household income (MTAG)	2.000000e-11
GCST009524_314	Household income (MTAG)	2.000000e-09
GCST009543_8	Cleft lip with or without cleft palate x maternal periconceptional vitamin use interaction (parent of origin effect)	4.000000e-06
GCST011319_1	Interstitial lung diseases in rheumatoid arthritis	2.000000e-08
GCST012226_696	Waist circumference adjusted for body mass index	4.000000e-08
GCST012227_105	Hip circumference adjusted for BMI	2.000000e-10
GCST012490_200	Femur bone mineral density x serum urate levels interaction	1.000000e-09
GCST90002379_145	Basophil count	2.000000e-20
GCST90002380_42	Basophil percentage of white cells	1.000000e-13
GCST90002381_173	Eosinophil count	9.000000e-10
GCST90002394_185	Monocyte percentage of white cells	8.000000e-10
GCST90002399_166	Neutrophil percentage of white cells	3.000000e-13

EFO canonical traits (17, from GWAS)

EFO ID	Trait name
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0007987	granulocyte count
EFO:0005090	basophil count
EFO:0005035	hippocampal volume
EFO:0004695	intraocular pressure measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0006781	coffee consumption measurement
EFO:0009695	household income
EFO:0003959	cleft lip
EFO:0005939	parental genotype effect measurement
EFO:0009116	vitamin supplement exposure measurement
EFO:0007789	BMI-adjusted waist circumference
EFO:0004531	urate measurement
EFO:0007992	basophil percentage of leukocytes
EFO:0007989	monocyte percentage of leukocytes
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, affects methylation, decreases methylation, affects expression, increases abundance	2
trichostatin A	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
ginger extract	affects cotreatment, affects expression, increases abundance	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Air Pollutants	increases abundance, affects expression	1
Doxorubicin	decreases expression	1
Oils, Volatile	increases abundance, affects cotreatment, affects expression	1
Ozone	affects expression, increases abundance	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1
Valproic Acid	affects expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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