UNC93A

Summary

UNC93A (unc-93 homolog A, HGNC:12570) is a protein-coding gene on chromosome 6q27, encoding Protein unc-93 homolog A (Q86WB7).

Located in plasma membrane.

Source: NCBI Gene 54346 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 99 total
• Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
• MANE Select transcript: NM_018974

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12570
Approved symbol	UNC93A
Name	unc-93 homolog A
Location	6q27
Locus type	gene with protein product
Status	Approved
Aliases	dJ366N23.2, dJ366N23.1
Ensembl gene	ENSG00000112494
Ensembl biotype	protein_coding
OMIM	607995
Entrez	54346

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000230256, ENST00000366829, ENST00000366830, ENST00000503433, ENST00000504706, ENST00000860147

RefSeq mRNA: 2 — MANE Select: NM_018974 NM_001143947, NM_018974

CCDS: CCDS47515, CCDS5300

Canonical transcript exons

ENST00000230256 — 8 exons

Exon	Start	End
ENSE00000765849	167303919	167304133
ENSE00000765850	167305915	167306050
ENSE00000765851	167307779	167307910
ENSE00001152127	167297945	167298070
ENSE00001257818	167291315	167291576
ENSE00001257825	167315187	167316014
ENSE00003570582	167294517	167294698
ENSE00003682092	167296032	167296261

Expression profiles

Bgee: expression breadth broad, 73 present calls, max score 84.05.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4744 / max 265.3771, expressed in 77 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
71194	0.1975	52
71193	0.1297	11
71198	0.0589	13
71197	0.0386	13
71196	0.0240	10
71195	0.0143	4
71192	0.0113	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	84.05	gold quality
secondary oocyte	CL:0000655	81.83	gold quality
skin of abdomen	UBERON:0001416	81.74	gold quality
zone of skin	UBERON:0000014	78.30	gold quality
right lobe of liver	UBERON:0001114	75.77	gold quality
buccal mucosa cell	CL:0002336	74.45	gold quality
lower esophagus mucosa	UBERON:0035834	69.38	gold quality
esophagus mucosa	UBERON:0002469	68.72	gold quality
oocyte	CL:0000023	68.32	gold quality
duodenum	UBERON:0002114	65.14	gold quality
liver	UBERON:0002107	64.98	gold quality
small intestine	UBERON:0002108	55.31	gold quality
rectum	UBERON:0001052	55.08	gold quality
small intestine Peyer’s patch	UBERON:0003454	54.36	gold quality
gall bladder	UBERON:0002110	51.67	gold quality
jejunal mucosa	UBERON:0000399	51.51	silver quality
adult mammalian kidney	UBERON:0000082	51.14	gold quality
frontal pole	UBERON:0002795	50.41	gold quality
middle frontal gyrus	UBERON:0002702	50.30	gold quality
paraflocculus	UBERON:0005351	50.18	gold quality
Brodmann (1909) area 10	UBERON:0013541	50.18	gold quality
metanephros	UBERON:0000081	49.79	gold quality
upper leg skin	UBERON:0004262	49.70	gold quality
quadriceps femoris	UBERON:0001377	49.65	gold quality
oviduct epithelium	UBERON:0004804	49.47	gold quality
lower lobe of lung	UBERON:0008949	49.43	silver quality
esophagus	UBERON:0001043	49.32	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
cerebellar vermis	UBERON:0004720	49.25	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting UNC93A, 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-4283	100.00	66.42	2097
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-3064-5P	99.26	66.13	1497
HSA-MIR-3085-3P	99.26	66.16	1490
HSA-MIR-6504-5P	99.26	65.95	1487
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-4426	99.17	66.74	1949
HSA-MIR-3926	98.95	69.26	1438
HSA-MIR-1294	98.91	69.26	1030
HSA-MIR-9986	98.91	69.28	1024
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-640	98.44	66.93	644
HSA-MIR-4724-3P	97.57	67.31	785
HSA-MIR-1225-3P	97.29	64.60	876
HSA-MIR-3684	96.90	67.51	293
HSA-MIR-4695-3P	96.71	67.21	836
HSA-MIR-5702	96.68	68.21	958
HSA-MIR-3675-5P	95.90	65.80	474
HSA-MIR-4522	95.76	66.23	742
HSA-MIR-8071	95.69	64.93	484
HSA-MIR-5586-3P	95.51	67.00	805

Functional genomics

ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 1)

• Results suggest that no evidence for UNC93A as a tumour suppressor gene in sporadic ovarian cancer has been identified and further research is required to evaluate its normal function and role in the pathogenesis of ovarian cancer. (PMID:12381271)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	unc93a	ENSDARG00000041554
mus_musculus	Unc93a2	ENSMUSG00000056133
mus_musculus	Unc93a	ENSMUSG00000067049
rattus_norvegicus	Unc93a	ENSRNOG00000047027
drosophila_melanogaster	CG4928	FBGN0027556
drosophila_melanogaster	CG2121	FBGN0033289
caenorhabditis_elegans		WBGENE00006822

Paralogs (1): UNC93B1 (ENSG00000110057)

Protein

Protein identifiers

Protein unc-93 homolog A — Q86WB7 (reviewed: Q86WB7)

All UniProt accessions (2): Q86WB7, D6RFH7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell membrane.

Tissue specificity. Expressed in testis, small intestine, spleen, prostate and ovary.

Miscellaneous. Although UNC93A gene is located in a region of the genome frequently associated with ovarian cancer, no evidence have been found for a tumor suppressor function.

Similarity. Belongs to the unc-93 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86WB7-1	1	yes
Q86WB7-2	2

RefSeq proteins (2): NP_001137419, NP_061847* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010291	Ion_channel_UNC-93	Family
IPR036259	MFS_trans_sf	Homologous_superfamily
IPR051951	UNC-93_regulatory	Family

Pfam: PF05978

UniProt features (24 total): transmembrane region 11, sequence variant 10, chain 1, glycosylation site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86WB7-F1	85.04	0.53

Functional residue map

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

Glycosylation sites (1): 190

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 23 (showing top): BROWNE_HCMV_INFECTION_14HR_DN, BROWNE_HCMV_INFECTION_6HR_UP, chr6q27, MARTENS_TRETINOIN_RESPONSE_UP, SUMI_HNF4A_TARGETS, MIR3120_3P, MIR3926, GSE12845_NAIVE_VS_DARKZONE_GC_TONSIL_BCELL_UP, TBX3_TARGET_GENES, CAIRO_HEPATOBLASTOMA_CLASSES_UP, GSE360_CTRL_VS_T_GONDII_MAC_DN, GSE360_T_GONDII_VS_M_TUBERCULOSIS_DC_UP, GSE360_L_DONOVANI_VS_B_MALAYI_LOW_DOSE_MAC_UP, GSE360_L_MAJOR_VS_B_MALAYI_HIGH_DOSE_MAC_DN, GSE360_T_GONDII_VS_B_MALAYI_LOW_DOSE_MAC_UP

GO Biological Process (0):

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

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

578 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UNC93A	SLC67A2	Q8NBP5	692
UNC93A	SVOPL	Q8N434	637
UNC93A	SVOP	Q8N4V2	618
UNC93A	SLC75A1	Q14728	614
UNC93A	SLC68A1	Q14CX5	578
UNC93A	SLC61A1	Q6N075	568
UNC93A	MFSD6	Q6ZSS7	560
UNC93A	MFSD6L	Q8IWD5	548
UNC93A	SLC71A1	Q96MC6	545
UNC93A	MFSD12	Q6NUT3	530
UNC93A	B9ZVM9	B9ZVM9	528
UNC93A	Q12799	Q12799	527
UNC93A	SLC33A2	Q96ES6	521
UNC93A	SPNS3	Q6ZMD2	495
UNC93A	MFSD1	Q9H3U5	489

IntAct

128 interactions, top by confidence:

A	B	Type	Score
PDZK1	UNC93A	psi-mi:“MI:0407”(direct interaction)	0.440
MAST2	UNC93A	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	SHANK1	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	NHERF2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	PDZK1	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
PICK1	UNC93A	psi-mi:“MI:0407”(direct interaction)	0.440
APBA3	UNC93A	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	MPP2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	TIAM2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	PCLO	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	TAX1BP3	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	LNX2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	RAPGEF6	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	PALS2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	TJP3	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	MPP7	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	GRID2IP	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	NHERF4	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	PDZRN4	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	FRMPD2	psi-mi:“MI:0407”(direct interaction)	0.440
UNC93A	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (65): UNC93A (Affinity Capture-MS), UNC93A (Two-hybrid), UNC93A (Two-hybrid), UNC93A (Two-hybrid), UNC93A (Two-hybrid), UNC93A (Two-hybrid), UNC93A (Two-hybrid), UNC93A (Two-hybrid), LNPEP (Two-hybrid), TIMMDC1 (Two-hybrid), GJA8 (Two-hybrid), TMEM14B (Two-hybrid), TMEM237 (Two-hybrid), FCER1G (Two-hybrid), GPR101 (Two-hybrid)

ESM2 similar proteins: A0A0R4ILB2, A0A8M9Q308, A1A4N1, A2CER7, A5D7V7, A8WGF7, B0S5Y3, B2RXV4, B5X4H8, O00400, O00476, O01735, O23596, P30638, P36836, P46029, P60815, Q11073, Q16348, Q28722, Q28FF3, Q503P5, Q5F4B8, Q5RBM3, Q5XGK0, Q63424, Q6AYY8, Q6DDL7, Q6DIT7, Q6GMG6, Q6PB15, Q7Z3Q1, Q84XI3, Q86WB7, Q91X85, Q944P0, Q99808, Q99J27, Q9BZD2, Q9C8X2

Diamond homologs: A2VE54, Q5SPF7, Q6DDL7, Q710D3, Q86WB7, Q93380, Q9Y115, Q8BJ51

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 81 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
Ras activation upon Ca2+ influx through NMDA receptor	5	52.9×	1e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	50.4×	1e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	50.4×	1e-06
Assembly and cell surface presentation of NMDA receptors	10	47.0×	7e-13
Dopamine Neurotransmitter Release Cycle	5	46.0×	2e-06
Long-term potentiation	5	44.1×	2e-06
Neurexins and neuroligins	11	40.1×	4e-13
Protein-protein interactions at synapses	7	34.4×	7e-08

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	82.0×	2e-16
protein localization to synapse	6	58.9×	7e-08
receptor clustering	7	56.0×	7e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	7	44.5×	3e-08
protein-containing complex assembly	9	13.1×	2e-06
cell-cell adhesion	10	13.0×	4e-07
chemical synaptic transmission	7	6.9×	2e-03
protein transport	8	4.5×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	81
Likely benign	8
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

2169 predictions. Top by Δscore:

Variant	Effect	Δscore
6:167294695:GCTG:G	donor_gain	1.0000
6:167313491:G:GT	donor_gain	1.0000
6:167313495:G:GT	donor_gain	1.0000
6:167313496:G:T	donor_gain	1.0000
6:167315183:GCAGC:G	acceptor_loss	1.0000
6:167315184:CA:C	acceptor_loss	1.0000
6:167315185:A:AG	acceptor_gain	1.0000
6:167315186:G:GG	acceptor_gain	1.0000
6:167291575:AGGT:A	donor_loss	0.9900
6:167291576:GG:G	donor_loss	0.9900
6:167291578:T:A	donor_loss	0.9900
6:167294515:A:AG	acceptor_gain	0.9900
6:167294516:G:GG	acceptor_gain	0.9900
6:167294516:GAGCA:G	acceptor_gain	0.9900
6:167297090:T:A	acceptor_gain	0.9900
6:167297093:T:A	acceptor_gain	0.9900
6:167304132:GG:G	donor_gain	0.9900
6:167304133:GG:G	donor_gain	0.9900
6:167305913:A:AG	acceptor_gain	0.9900
6:167305914:G:GA	acceptor_gain	0.9900
6:167305914:GTCCT:G	acceptor_gain	0.9900
6:167315186:GCT:G	acceptor_gain	0.9900
6:167315186:GCTCT:G	acceptor_gain	0.9900
6:167294516:GA:G	acceptor_gain	0.9800
6:167294696:CTGG:C	donor_loss	0.9800
6:167294698:GGTAC:G	donor_loss	0.9800
6:167294699:G:GG	donor_gain	0.9800
6:167294699:GTA:G	donor_loss	0.9800
6:167294700:T:C	donor_loss	0.9800
6:167297011:T:G	acceptor_gain	0.9800

AlphaMissense

2941 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:167291544:T:C	F19L	0.986
6:167291546:T:A	F19L	0.986
6:167291546:T:G	F19L	0.986
6:167315228:T:C	F384L	0.986
6:167315230:C:A	F384L	0.986
6:167315230:C:G	F384L	0.986
6:167315204:T:C	F376L	0.981
6:167315206:T:A	F376L	0.981
6:167315206:T:G	F376L	0.981
6:167291532:T:C	F15L	0.975
6:167291534:C:A	F15L	0.975
6:167291534:C:G	F15L	0.975
6:167315258:G:C	G394R	0.974
6:167315259:G:A	G394D	0.972
6:167294559:A:C	S44R	0.971
6:167294561:C:A	S44R	0.971
6:167294561:C:G	S44R	0.971
6:167294520:A:C	S31R	0.970
6:167294522:C:A	S31R	0.970
6:167294522:C:G	S31R	0.970
6:167294670:T:C	F81L	0.970
6:167294672:C:A	F81L	0.970
6:167294672:C:G	F81L	0.970
6:167291572:T:C	L28P	0.968
6:167296063:G:A	G101R	0.967
6:167296063:G:C	G101R	0.967
6:167296213:T:A	W151R	0.966
6:167296213:T:C	W151R	0.966
6:167296090:G:C	A110P	0.965
6:167315226:C:A	A383D	0.964

dbSNP variants (sampled 300 via entrez): RS1000022843 (6:167280920 C>G), RS1000035796 (6:167287338 C>A,G,T), RS1000078011 (6:167276354 G>C), RS1000151414 (6:167267952 T>C), RS1000181623 (6:167280519 A>G), RS1000193232 (6:167276563 C>G,T), RS1000214713 (6:167306403 C>T), RS1000232584 (6:167280688 C>A,T), RS1000289466 (6:167294328 G>T), RS1000427222 (6:167289392 A>G), RS1000499500 (6:167296710 T>G), RS1000508845 (6:167267787 T>A), RS1000614075 (6:167296957 A>G), RS1000698504 (6:167285435 A>G), RS1000710493 (6:167290433 G>A,T)

Disease associations

OMIM: gene MIM:607995 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST006633_16	Initial alcohol sensitivity	3.000000e-06
GCST009733_170	Urinary metabolite levels in chronic kidney disease	7.000000e-33
GCST009733_171	Urinary metabolite levels in chronic kidney disease	2.000000e-46
GCST012020_10	Serum metabolite levels	2.000000e-33
GCST012020_11	Serum metabolite levels	4.000000e-49
GCST012020_12	Serum metabolite levels	3.000000e-17

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005116	urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, affects cotreatment, decreases methylation	2
(+)-JQ1 compound	decreases expression	2
Aflatoxin B1	decreases expression, decreases methylation	2
OTX015	decreases expression	1
mivebresib	decreases expression	1
benzo(e)pyrene	increases methylation	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
belinostat	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Diethylnitrosamine	decreases expression	1
Methapyrilene	increases methylation	1
Phenylmercuric Acetate	affects cotreatment, increases expression	1
Urethane	decreases expression	1
Valproic Acid	increases expression	1
Lactic Acid	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4V0	HuH7-UNC93A-KO-c11	Cancer cell line	Male
CVCL_D4V1	HuH7-UNC93A-KO-c3	Cancer cell line	Male

Clinical trials (associated diseases)

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