TBC1D2B

Summary

TBC1D2B (TBC1 domain family member 2B, HGNC:29183) is a protein-coding gene on chromosome 15q24.3-q25.1, encoding TBC1 domain family member 2B (Q9UPU7). GTPase-activating protein that plays a role in the early steps of endocytosis.

Predicted to enable GTPase activator activity. Involved in endocytosis. Located in cytosol and early endosome.

Source: NCBI Gene 23102 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder with seizures and gingival overgrowth (Strong, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 183 total — 5 pathogenic, 5 likely-pathogenic
• Phenotypes (HPO): 20
• MANE Select transcript: NM_144572

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29183
Approved symbol	TBC1D2B
Name	TBC1 domain family member 2B
Location	15q24.3-q25.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1055
Ensembl gene	ENSG00000167202
Ensembl biotype	protein_coding
OMIM	619152
Entrez	23102

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 9 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000300584, ENST00000409931, ENST00000418039, ENST00000435468, ENST00000459715, ENST00000465531, ENST00000472786, ENST00000482562, ENST00000486703, ENST00000491479, ENST00000492078, ENST00000497942, ENST00000936499, ENST00000936500, ENST00000971560, ENST00000971561, ENST00000971562

RefSeq mRNA: 10 — MANE Select: NM_144572 NM_001387142, NM_001387143, NM_001387144, NM_001387145, NM_001387146, NM_001387147, NM_001387148, NM_001387149, NM_015079, NM_144572

CCDS: CCDS32301, CCDS45314

Canonical transcript exons

ENST00000300584 — 13 exons

Exon	Start	End
ENSE00001110909	78017847	78017957
ENSE00001110911	78016546	78016739
ENSE00001110917	78024156	78024539
ENSE00001110918	78001619	78001740
ENSE00001110919	78003305	78003490
ENSE00001160265	78025259	78025497
ENSE00001160274	78030007	78030170
ENSE00001160285	78044900	78045068
ENSE00001614666	78077293	78077711
ENSE00001698153	78054034	78054187
ENSE00001770597	77994985	77998355
ENSE00003651406	78008997	78009114
ENSE00003690202	78012823	78013317

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 95.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.2873 / max 208.2473, expressed in 1778 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
151093	9.1928	1762
151092	3.8496	1233
151091	0.2094	101
151087	0.0355	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	95.98	gold quality
left ovary	UBERON:0002119	95.96	gold quality
right ovary	UBERON:0002118	95.51	gold quality
mucosa of stomach	UBERON:0001199	95.48	gold quality
right lung	UBERON:0002167	95.25	gold quality
endocervix	UBERON:0000458	95.13	gold quality
right coronary artery	UBERON:0001625	94.57	gold quality
ovary	UBERON:0000992	94.17	gold quality
upper lobe of left lung	UBERON:0008952	94.12	gold quality
gall bladder	UBERON:0002110	93.71	gold quality
subcutaneous adipose tissue	UBERON:0002190	93.67	gold quality
upper lobe of lung	UBERON:0008948	93.66	gold quality
popliteal artery	UBERON:0002250	93.52	gold quality
tibial artery	UBERON:0007610	93.51	gold quality
calcaneal tendon	UBERON:0003701	93.45	gold quality
adipose tissue of abdominal region	UBERON:0007808	93.21	gold quality
adipose tissue	UBERON:0001013	93.20	gold quality
omental fat pad	UBERON:0010414	93.19	gold quality
peritoneum	UBERON:0002358	93.18	gold quality
stromal cell of endometrium	CL:0002255	92.95	gold quality
saphenous vein	UBERON:0007318	92.94	gold quality
connective tissue	UBERON:0002384	92.86	gold quality
body of uterus	UBERON:0009853	92.74	gold quality
periodontal ligament	UBERON:0008266	92.60	gold quality
coronary artery	UBERON:0001621	92.48	gold quality
lymph node	UBERON:0000029	92.46	gold quality
tibial nerve	UBERON:0001323	92.34	gold quality
spleen	UBERON:0002106	92.32	gold quality
lung	UBERON:0002048	92.30	gold quality
aorta	UBERON:0000947	92.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

145 targeting TBC1D2B, 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-3163	100.00	77.23	8605
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-4673	100.00	66.64	1490
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4692	100.00	67.32	2066
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-8485	100.00	77.57	4731
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-4267	99.96	66.53	2368

Literature-anchored findings (GeneRIF, showing 3)

• TBC1D2b suppresses E-cadherin internalization, thus hindering cancer cell invasion and metastasis. (PMID:31719531)
• Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth. (PMID:32623794)
• Biallelic frameshift variant in the TBC1D2B gene in two siblings with progressive gingival overgrowth, fibrous dysplasia of face, and mental deterioration. (PMID:36029130)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tbc1d2b	ENSDARG00000061986
mus_musculus	Tbc1d2b	ENSMUSG00000037410
rattus_norvegicus	Tbc1d2b	ENSRNOG00000014543

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D2 (ENSG00000095383), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D17 (ENSG00000104946), TBC1D13 (ENSG00000107021), TBC1D12 (ENSG00000108239), TBC1D9 (ENSG00000109436), TBC1D30 (ENSG00000111490), TBC1D15 (ENSG00000121749), TBC1D5 (ENSG00000131374), TBC1D14 (ENSG00000132405), TBC1D8B (ENSG00000133138), TBC1D4 (ENSG00000136111), GRTP1 (ENSG00000139835), SGSM2 (ENSG00000141258), EVI5L (ENSG00000142459), TBCK (ENSG00000145348), USP6NL (ENSG00000148429), RABGAP1L (ENSG00000152061), SGSM1 (ENSG00000167037), TBC1D21 (ENSG00000167139), TBC1D16 (ENSG00000167291), TBC1D10B (ENSG00000169221), TBC1D10C (ENSG00000175463), TBC1D28 (ENSG00000189375), TBC1D9B (ENSG00000197226), TBC1D8 (ENSG00000204634), TBC1D26 (ENSG00000214946), TBC1D3G (ENSG00000260287), TBC1D3K (ENSG00000273513), TBC1D3H (ENSG00000274226), TBC1D3D (ENSG00000274419), TBC1D3L (ENSG00000274512), TBC1D3 (ENSG00000274611)

Protein

Protein identifiers

TBC1 domain family member 2B — Q9UPU7 (reviewed: Q9UPU7)

All UniProt accessions (3): C9JW56, Q9UPU7, H0YL97

UniProt curated annotations — full annotation on UniProt →

Function. GTPase-activating protein that plays a role in the early steps of endocytosis.

Subcellular location. Early endosome.

Disease relevance. Neurodevelopmental disorder with seizures and gingival overgrowth (NEDSGO) [MIM:619323] An autosomal recessive disorder with variable clinical manifestations including delayed development, hypotonia, seizures, gingival hypertrophy associated with a prominent mandible or cherubism in the first years of life. Some patients have early normal development followed by developmental regression. Additional variable features are coarse facial features, optic atrophy, sensorineural hearing loss, and ataxia. Brain imaging may show cerebellar or cerebral atrophy and enlarged ventricles. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9UPU7-1	1	yes
Q9UPU7-2	2
Q9UPU7-3	3

RefSeq proteins (10): NP_001374071, NP_001374072, NP_001374073, NP_001374074, NP_001374075, NP_001374076, NP_001374077, NP_001374078, NP_055894, NP_653173* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000195	Rab-GAP-TBC_dom	Domain
IPR001849	PH_domain	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR035969	Rab-GAP_TBC_sf	Homologous_superfamily
IPR050302	Rab_GAP_TBC_domain	Family

Pfam: PF00169, PF00566

UniProt features (24 total): sequence variant 8, modified residue 4, splice variant 4, domain 2, region of interest 2, compositionally biased region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UPU7-F1	71.68	0.32

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 (4): 473, 957, 155, 317

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 249 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, MODULE_45, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, CAGCTG_AP4_Q5, MODULE_503, CAIRO_HEPATOBLASTOMA_CLASSES_DN, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, MODULE_195, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, MODULE_88, MODULE_147, GOBP_REGULATION_OF_CILIUM_ASSEMBLY

GO Biological Process (1): endocytosis (GO:0006897)

GO Molecular Function (2): GTPase activator activity (GO:0005096), protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), early endosome (GO:0005769), cytosol (GO:0005829), plasma membrane (GO:0005886), endosome (GO:0005768), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cytoplasm	2
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
binding	1
intracellular anatomical structure	1
endosome	1
membrane	1
cell periphery	1
endomembrane system	1
cytoplasmic vesicle	1
intracellular vesicle	1

Protein interactions and networks

STRING

1674 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TBC1D2B	RAB31	Q13636	737
TBC1D2B	RAB22A	Q9UL26	562
TBC1D2B	TBC1D19	Q8N5T2	530
TBC1D2B	TBC1D25	Q3MII6	525
TBC1D2B	TBC1D21	Q8IYX1	523
TBC1D2B	TBC1D13	Q9NVG8	514
TBC1D2B	RAB35	Q15286	496
TBC1D2B	TBC1D5	Q92609	475
TBC1D2B	CDC16	Q13042	437
TBC1D2B	TBC1D28	Q2M2D7	418
TBC1D2B	TBC1D23	Q9NUY8	400
TBC1D2B	RAB36	O95755	398
TBC1D2B	RAB5A	P20339	373
TBC1D2B	MEPCE	Q7L2J0	365
TBC1D2B	CCZ1B	P86790	361

IntAct

88 interactions, top by confidence:

A	B	Type	Score
PSMC3	PSMD9	psi-mi:“MI:0914”(association)	0.940
RFXANK	RFXAP	psi-mi:“MI:0914”(association)	0.780
PSMC3	PSMD12	psi-mi:“MI:0914”(association)	0.640
TBC1D2B	GABARAPL1	psi-mi:“MI:0407”(direct interaction)	0.590
TBC1D2B	GABARAPL2	psi-mi:“MI:0407”(direct interaction)	0.590
TBC1D2B	MAP1LC3B	psi-mi:“MI:0407”(direct interaction)	0.590
TBC1D2B	GABARAPL1	psi-mi:“MI:0915”(physical association)	0.590
GABARAPL2	TBC1D2B	psi-mi:“MI:0915”(physical association)	0.590
MAP1LC3B	TBC1D2B	psi-mi:“MI:0915”(physical association)	0.590
GABARAPL1	IPO5	psi-mi:“MI:0914”(association)	0.590
GABARAP	TBC1D2B	psi-mi:“MI:0407”(direct interaction)	0.540
MAP1LC3C	TBC1D2B	psi-mi:“MI:0407”(direct interaction)	0.540
TBC1D2B	GABARAP	psi-mi:“MI:0915”(physical association)	0.540
TBC1D2B	MAP1LC3C	psi-mi:“MI:0915”(physical association)	0.540
WASHC3	WASH3P	psi-mi:“MI:0914”(association)	0.530
KLHL40	CBX4	psi-mi:“MI:0914”(association)	0.530
COG6	EXOC5	psi-mi:“MI:0914”(association)	0.530
ALOX5	DDHD2	psi-mi:“MI:0914”(association)	0.530
HSPB8	VWA8	psi-mi:“MI:0914”(association)	0.530
ASB6	POLR2D	psi-mi:“MI:0914”(association)	0.530
LURAP1	TRIM24	psi-mi:“MI:0914”(association)	0.530
TBC1D2B	S100A6	psi-mi:“MI:0915”(physical association)	0.400
TRDMT1	TBC1D2B	psi-mi:“MI:0915”(physical association)	0.370
TBC1D2B		psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
CAV3	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (111): TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Proximity Label-MS), TBC1D2B (Proximity Label-MS), TBC1D2B (Proximity Label-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2JXN2, A2AWP8, O88842, O95267, P29590, P52734, P98174, Q1LY10, Q29RM4, Q2TBA3, Q3TAA7, Q3U0J8, Q3UTZ3, Q496Y0, Q4VX76, Q568M3, Q58D15, Q5BIM1, Q5JSP0, Q5R5M3, Q5R5T1, Q5REJ9, Q5W0U4, Q68FF6, Q69Z89, Q69ZK0, Q6PFY8, Q7TNM2, Q7Z4K8, Q7Z5H3, Q7Z6J4, Q80V85, Q8BY35, Q8BZ52, Q8C190, Q8N1F8, Q8TCU6, Q8WVR3, Q96JH8, Q99N48

Diamond homologs: A1A5K6, A5PKL1, Q08CX5, Q29RJ2, Q3UUG6, Q9ULP9, Q9UPU7, Q9VIH7, A2AWA9, A3KGB4, A6H6A9, A6H8I2, A6QP29, B0R0W9, B1AVH7, B5DFA1, C8VDQ4, D2H0G5, F4HVW5, O60447, O95759, P53258, P58802, P87234, Q0IIM8, Q12317, Q28CB1, Q2KI13, Q3KR37, Q3KR56, Q3U0J8, Q3UYK3, Q4KMP7, Q4QQU7, Q5R372, Q5RAN1, Q5RCW6, Q5SVR0, Q5TC63, Q66K14

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 106 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
Macroautophagy	6	11.7×	5e-03

GO biological processes:

GO term	Partners	Fold	FDR
autophagosome maturation	6	22.6×	8e-05
mitophagy	6	20.5×	9e-05
autophagosome assembly	6	14.5×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	5
Uncertain significance	130
Likely benign	22
Benign	2

Top pathogenic / likely-pathogenic (10)

Variant ID	HGVS	Classification
1098844	NM_144572.2(TBC1D2B):c.2378T>A (p.Leu793Ter)	Pathogenic
1098845	NM_144572.2(TBC1D2B):c.426dup (p.Asn143Ter)	Pathogenic
1098846	NM_144572.2(TBC1D2B):c.1480C>T (p.Gln494Ter)	Pathogenic
1098847	NM_144572.2(TBC1D2B):c.658_659del (p.Leu220fs)	Pathogenic
1098848	NM_144572.2(TBC1D2B):c.2295C>G (p.Tyr765Ter)	Pathogenic
1683745	NM_144572.2(TBC1D2B):c.425delinsTT (p.Cys142fs)	Likely pathogenic
2633315	NM_144572.2(TBC1D2B):c.2016G>A (p.Trp672Ter)	Likely pathogenic
3058247	NM_144572.2(TBC1D2B):c.2353C>T (p.Arg785Ter)	Likely pathogenic
3059042	NM_144572.2(TBC1D2B):c.159C>G (p.Tyr53Ter)	Likely pathogenic
4278061	NM_144572.2(TBC1D2B):c.1491_1503del (p.Lys497fs)	Likely pathogenic

SpliceAI

2567 predictions. Top by Δscore:

Variant	Effect	Δscore
15:77998365:C:CT	acceptor_gain	1.0000
15:77998367:C:CT	acceptor_gain	1.0000
15:78001612:GACTC:G	donor_loss	1.0000
15:78001613:ACTC:A	donor_loss	1.0000
15:78001614:CTCA:C	donor_loss	1.0000
15:78001615:TCACC:T	donor_loss	1.0000
15:78001616:CA:C	donor_loss	1.0000
15:78001660:A:AC	donor_gain	1.0000
15:78001661:A:C	donor_gain	1.0000
15:78001737:TAACC:T	acceptor_loss	1.0000
15:78001739:ACC:A	acceptor_loss	1.0000
15:78001742:T:A	acceptor_loss	1.0000
15:78003301:TCAC:T	donor_loss	1.0000
15:78003302:CA:C	donor_loss	1.0000
15:78003303:A:T	donor_loss	1.0000
15:78003304:C:CG	donor_loss	1.0000
15:78003375:A:AC	donor_gain	1.0000
15:78003376:C:CG	donor_gain	1.0000
15:78003377:C:CC	donor_gain	1.0000
15:78003487:CCAC:C	acceptor_gain	1.0000
15:78003488:CAC:C	acceptor_gain	1.0000
15:78003488:CACC:C	acceptor_gain	1.0000
15:78003489:AC:A	acceptor_gain	1.0000
15:78003489:ACCT:A	acceptor_loss	1.0000
15:78003490:CC:C	acceptor_gain	1.0000
15:78003491:C:CC	acceptor_gain	1.0000
15:78003491:CTG:C	acceptor_loss	1.0000
15:78003492:T:C	acceptor_loss	1.0000
15:78012818:CCCA:C	donor_loss	1.0000
15:78012819:CCA:C	donor_loss	1.0000

AlphaMissense

6333 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:77998257:A:G	L932P	0.999
15:78003334:A:G	W849R	0.999
15:78003334:A:T	W849R	0.999
15:78003388:A:G	W831R	0.999
15:78003388:A:T	W831R	0.999
15:78009010:A:G	L792P	0.999
15:78012825:G:C	N756K	0.999
15:78012825:G:T	N756K	0.999
15:78012833:C:G	G754R	0.999
15:78012834:T:A	Q753H	0.999
15:78012834:T:G	Q753H	0.999
15:78012842:A:G	Y751H	0.999
15:78012877:A:G	L739P	0.999
15:78012946:C:G	R716P	0.999
15:78012954:G:C	D713E	0.999
15:78012954:G:T	D713E	0.999
15:78012955:T:A	D713V	0.999
15:78012955:T:C	D713G	0.999
15:78012955:T:G	D713A	0.999
15:78012956:C:G	D713H	0.999
15:78012958:A:G	L712P	0.999
15:78013079:A:G	W672R	0.999
15:78013079:A:T	W672R	0.999
15:78013184:A:G	W637R	0.999
15:78013184:A:T	W637R	0.999
15:78017899:A:G	L510P	0.999
15:78017920:A:G	L503P	0.999
15:78017922:A:C	F502L	0.999
15:78017922:A:T	F502L	0.999
15:78017924:A:G	F502L	0.999

dbSNP variants (sampled 300 via entrez): RS1000022624 (15:78016312 T>C), RS1000073014 (15:78066368 T>C,G), RS1000106799 (15:78076535 A>C), RS1000118621 (15:78033609 A>T), RS1000185168 (15:78027910 T>C), RS1000251364 (15:77999158 A>C,G), RS1000291820 (15:78053653 T>A,C), RS1000300069 (15:78063822 G>A,C), RS1000301301 (15:78027684 C>T), RS1000347112 (15:78014815 G>A), RS1000407051 (15:78033421 G>A,T), RS1000421898 (15:78023895 A>G), RS1000526918 (15:78057261 G>A), RS1000562873 (15:78008042 C>G), RS1000575429 (15:78070394 T>C)

Disease associations

OMIM: gene MIM:619152 | disease phenotypes: MIM:619323

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder with seizures and gingival overgrowth	Strong	Autosomal recessive

Mondo (1): neurodevelopmental disorder with seizures and gingival overgrowth (MONDO:0859148)

Orphanet (0):

HPO phenotypes

20 total (20 of 20 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000212	Gingival overgrowth
HP:0000280	Coarse facial features
HP:0000648	Optic atrophy
HP:0000748	Inappropriate laughter
HP:0001250	Seizure
HP:0001256	Mild intellectual disability
HP:0001272	Cerebellar atrophy
HP:0001350	Slurred speech
HP:0002066	Gait ataxia
HP:0002119	Ventriculomegaly
HP:0002376	Developmental regression
HP:0005830	Flexion contracture of toe
HP:0008936	Axial hypotonia
HP:0011198	EEG with generalized epileptiform discharges
HP:0011463	Childhood onset
HP:0030215	Inappropriate crying
HP:0030793	Jaw swelling
HP:0033720	EEG with occipital epileptiform discharges
HP:0100490	Camptodactyly of finger

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003476_6	Eyebrow thickness	1.000000e-06
GCST007637_9	Diffusing capacity of carbon monoxide	3.000000e-10
GCST009391_576	Metabolite levels	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009369	diffusing capacity of the lung for carbon monoxide
EFO:0021604	hypoxanthine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects methylation, increases expression, affects cotreatment	3
sodium arsenite	decreases expression, increases abundance, increases expression	2
Acetaminophen	increases expression, decreases expression	2
Arsenic	affects methylation, decreases expression, increases abundance	2
Valproic Acid	decreases expression, decreases methylation, increases expression	2
Cyclosporine	decreases expression, increases methylation	2
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
beauvericin	affects cotreatment, decreases expression	1
beta-lapachone	increases expression	1
potassium chromate(VI)	decreases expression	1
beta-methylcholine	affects expression	1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
enniatins	affects cotreatment, decreases expression	1
2-palmitoylglycerol	increases expression	1
abrine	decreases expression	1
jinfukang	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	increases expression	1
Air Pollutants, Occupational	decreases expression	1
Benzene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Gallic Acid	decreases expression	1
Indomethacin	increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Phenobarbital	affects expression	1

Clinical trials (associated diseases)

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