TUBGCP5

Summary

TUBGCP5 (tubulin gamma complex component 5, HGNC:18600) is a protein-coding gene on chromosome 15q11.2, encoding Gamma-tubulin complex component 5 (Q96RT8). Component of the gamma-tubulin ring complex (gTuRC) which mediates microtubule nucleation. It is a common-essential gene (DepMap: required in 98.8% of cancer cell lines).

Enables microtubule binding activity. Involved in microtubule nucleation. Located in centrosome; ciliary basal body; and cytosol. Part of gamma-tubulin ring complex.

Source: NCBI Gene 114791 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 200 total
• Phenotypes (HPO): 1
• Cancer dependency (DepMap): dependent in 98.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_052903

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18600
Approved symbol	TUBGCP5
Name	tubulin gamma complex component 5
Location	15q11.2
Locus type	gene with protein product
Status	Approved
Aliases	GCP5, KIAA1899
Ensembl gene	ENSG00000275835
Ensembl biotype	protein_coding
OMIM	608147
Entrez	114791

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000610294, ENST00000612085, ENST00000613552, ENST00000614508, ENST00000615383, ENST00000615455, ENST00000620238, ENST00000620435, ENST00000622507, ENST00000861884, ENST00000861885, ENST00000861886, ENST00000939427, ENST00000939428, ENST00000959740

RefSeq mRNA: 9 — MANE Select: NM_052903 NM_001102610, NM_001354372, NM_001354373, NM_001354374, NM_001354375, NM_001354376, NM_001354377, NM_001354378, NM_052903

CCDS: CCDS73697, CCDS73698

Canonical transcript exons

ENST00000615383 — 23 exons

Exon	Start	End
ENSE00003711513	23006052	23006172
ENSE00003712119	23039398	23039569
ENSE00003712185	23003065	23003153
ENSE00003712551	23037099	23037152
ENSE00003713169	23006268	23006352
ENSE00003714431	23017773	23018041
ENSE00003717630	23011133	23011331
ENSE00003718357	23023947	23024193
ENSE00003719388	23021959	23022161
ENSE00003721072	23008699	23008881
ENSE00003724408	23004102	23004227
ENSE00003724945	23032728	23032824
ENSE00003728241	23019219	23019334
ENSE00003728312	23030885	23031020
ENSE00003731405	23009945	23010133
ENSE00003740544	23027192	23027306
ENSE00003741783	22999177	22999866
ENSE00003747328	23031950	23032029
ENSE00003747736	23000569	23000669
ENSE00003750145	23026116	23026205
ENSE00003752342	23036897	23037005
ENSE00003753546	23024737	23024830
ENSE00003791606	23005432	23005610

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 95.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.3548 / max 114.8289, expressed in 1804 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
148987	14.5796	1787
148986	1.2960	882
148989	0.7898	466
148988	0.6894	392

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	95.45	gold quality
calcaneal tendon	UBERON:0003701	91.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.13	gold quality
corpus callosum	UBERON:0002336	89.46	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.28	gold quality
endometrium	UBERON:0001295	88.14	gold quality
body of pancreas	UBERON:0001150	86.36	gold quality
tonsil	UBERON:0002372	86.18	gold quality
endocervix	UBERON:0000458	86.15	gold quality
smooth muscle tissue	UBERON:0001135	85.19	gold quality
thyroid gland	UBERON:0002046	85.11	gold quality
adrenal gland	UBERON:0002369	85.11	gold quality
tibial nerve	UBERON:0001323	85.09	gold quality
pancreas	UBERON:0001264	85.05	gold quality
right adrenal gland cortex	UBERON:0035827	85.05	gold quality
right adrenal gland	UBERON:0001233	85.03	gold quality
right lobe of thyroid gland	UBERON:0001119	84.90	gold quality
uterine cervix	UBERON:0000002	84.84	gold quality
left adrenal gland	UBERON:0001234	84.82	gold quality
skeletal muscle tissue	UBERON:0001134	84.73	gold quality
left lobe of thyroid gland	UBERON:0001120	84.70	gold quality
left ovary	UBERON:0002119	84.70	gold quality
skin of leg	UBERON:0001511	84.60	gold quality
subcutaneous adipose tissue	UBERON:0002190	84.60	gold quality
adrenal tissue	UBERON:0018303	84.59	gold quality
muscle tissue	UBERON:0002385	84.52	gold quality
zone of skin	UBERON:0000014	84.49	gold quality
left adrenal gland cortex	UBERON:0035825	84.48	gold quality
ovary	UBERON:0000992	84.39	gold quality
right ovary	UBERON:0002118	84.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting TUBGCP5, 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-1250-3P	99.96	70.04	4038
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-888-3P	99.53	69.77	1057
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-1272	99.34	68.79	878
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-6878-3P	99.24	64.23	920
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-3138	98.41	67.53	744
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-214-5P	97.34	66.50	617
HSA-MIR-6836-3P	97.08	64.99	712
HSA-MIR-600	97.07	66.73	1259
HSA-MIR-6730-3P	97.03	67.54	889
HSA-MIR-6866-5P	96.64	68.06	624
HSA-MIR-1231	95.10	65.63	663

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• located in the genomic domain between break points 1 and 2 on chromosome 15, of the Prader-Willi/Angelman syndromes (PMID:14508708)
• quantitated mRNA levels of NIPA2, NIPA2,l CYFIP1, and GCP5 in Prader-Willi syndrome and correlated levels with psychological and behavior scales (PMID:16982806)
• GSK-3beta regulates the localization of gamma-tubulin ring complex, including GCP5, to the spindle poles, thereby controlling the formation of proper mitotic spindles (PMID:18316369)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	tubgcp5	ENSDARG00000077442
mus_musculus	Tubgcp5	ENSMUSG00000033790
rattus_norvegicus	Tubgcp5	ENSRNOG00000011480
drosophila_melanogaster	Grip128	FBGN0026433

Paralogs (4): TUBGCP3 (ENSG00000126216), TUBGCP6 (ENSG00000128159), TUBGCP2 (ENSG00000130640), TUBGCP4 (ENSG00000137822)

Protein

Protein identifiers

Gamma-tubulin complex component 5 — Q96RT8 (reviewed: Q96RT8)

All UniProt accessions (5): Q96RT8, A0A087WVL9, A0A087WVZ8, A0A087X006, A0A087X1Z1

UniProt curated annotations — full annotation on UniProt →

Function. Component of the gamma-tubulin ring complex (gTuRC) which mediates microtubule nucleation. The gTuRC regulates the minus-end nucleation of alpha-beta tubulin heterodimers that grow into microtubule protafilaments, a critical step in centrosome duplication and spindle formation.

Subunit / interactions. Component of the gamma-tubulin ring complex (gTuRC) consisting of TUBGCP2, TUBGCP3, TUBGCP4, TUBGCP5 and TUBGCP6 and gamma-tubulin TUBG1 or TUBG2. TUBGCP2, TUBGCP3, TUBGCP4, TUBGCP5 and TUBGCP6 assemble in a 5:5:2:1:1 stoichiometry; each is associated with a gamma-tubulin, thereby arranging 14 gamma-tubulins in a helical manner. Gamma-tubulin at the first position is blocked by TUBGCP3 at the last position, allowing 13 protafilaments to grow into a microtubule. The gTuRC (via TUBGCP3 and TUBGCP6) interacts with ACTB and MZT1; the interactions form a luminal bridge that stabilizes the initial structure during complex assembly. The gTuRC (via TUBGCP2) interacts with MZT2A/MZT2B and CDK5RAP2 (via CM1 motif); the interactions play a role in gTuRC activation.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Tissue specificity. Widely expressed, with highest levels in heart and skeletal muscle and moderate levels in brain.

Similarity. Belongs to the TUBGCP family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96RT8-1	1	yes
Q96RT8-2	2

RefSeq proteins (9): NP_001096080, NP_001341301, NP_001341302, NP_001341303, NP_001341304, NP_001341305, NP_001341306, NP_001341307, NP_443135* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007259	GCP	Family
IPR040457	GCP_C	Domain
IPR041470	GCP_N	Domain
IPR042241	GCP_C_sf	Homologous_superfamily
IPR059169	GCP5_N_ext	Domain

Pfam: PF04130, PF17681

UniProt features (14 total): helix 5, region of interest 2, compositionally biased region 2, sequence conflict 2, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

28 structures.

PDB	Method	Resolution (Å)
6L81	X-RAY DIFFRACTION	2.2
8RX1	ELECTRON MICROSCOPY	3.57
8Q62	ELECTRON MICROSCOPY	3.72
7AS4	ELECTRON MICROSCOPY	4.13
6V69	ELECTRON MICROSCOPY	4.2
6V6S	ELECTRON MICROSCOPY	4.3
9QVN	ELECTRON MICROSCOPY	4.7
7QJ0	ELECTRON MICROSCOPY	5.32
9QVM	ELECTRON MICROSCOPY	6.8
7QJ1	ELECTRON MICROSCOPY	7
8VRD	ELECTRON MICROSCOPY	7
7QJD	ELECTRON MICROSCOPY	7.1
7QJ3	ELECTRON MICROSCOPY	7.6
8VRJ	ELECTRON MICROSCOPY	7.7
7QJ6	ELECTRON MICROSCOPY	7.8
7QJE	ELECTRON MICROSCOPY	7.8
7QJ9	ELECTRON MICROSCOPY	8.1
8VRK	ELECTRON MICROSCOPY	8.5
7QJ2	ELECTRON MICROSCOPY	8.6
7QJ5	ELECTRON MICROSCOPY	8.7
7QJ7	ELECTRON MICROSCOPY	8.7
7QJ8	ELECTRON MICROSCOPY	8.7
7QJ4	ELECTRON MICROSCOPY	9
7QJA	ELECTRON MICROSCOPY	9.2
7QJB	ELECTRON MICROSCOPY	9.2
7QJC	ELECTRON MICROSCOPY	16.1
9I8G	ELECTRON MICROSCOPY	22.4
9I8H	ELECTRON MICROSCOPY	23.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96RT8-F1	69.81	0.03

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-380270	Recruitment of mitotic centrosome proteins and complexes
R-HSA-380320	Recruitment of NuMA to mitotic centrosomes

MSigDB gene sets: 0 (showing top):

GO Biological Process (6): mitotic cell cycle (GO:0000278), microtubule nucleation (GO:0007020), cytoplasmic microtubule organization (GO:0031122), spindle assembly (GO:0051225), meiotic cell cycle (GO:0051321), microtubule cytoskeleton organization (GO:0000226)

GO Molecular Function (4): microtubule binding (GO:0008017), gamma-tubulin binding (GO:0043015), protein binding (GO:0005515), microtubule minus-end binding (GO:0051011)

GO Cellular Component (12): spindle pole (GO:0000922), gamma-tubulin complex (GO:0000930), gamma-tubulin ring complex (GO:0000931), centrosome (GO:0005813), cytosol (GO:0005829), microtubule (GO:0005874), cilium (GO:0005929), ciliary transition zone (GO:0035869), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), microtubule organizing center (GO:0005815), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Centrosome maturation	1
Mitotic Prometaphase	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
microtubule organizing center	3
cell cycle	2
microtubule cytoskeleton organization	2
tubulin binding	2
microtubule cytoskeleton	2
cilium	2
mitotic nuclear division	1
microtubule polymerization	1
supramolecular fiber organization	1
spindle organization	1
chromosome segregation	1
membraneless organelle assembly	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
cytoskeleton organization	1
microtubule-based process	1
binding	1
microtubule binding	1
spindle	1
protein-containing complex	1
gamma-tubulin complex	1
gamma-tubulin small complex	1
centriole	1
cytoplasm	1
polymeric cytoskeletal fiber	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

730 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TUBGCP5	TUBGCP4	Q9UGJ1	998
TUBGCP5	NIPA2	Q8N8Q9	991
TUBGCP5	TUBGCP6	Q96RT7	987
TUBGCP5	NIPA1	Q7RTP0	983
TUBGCP5	CYFIP1	Q7L576	973
TUBGCP5	TUBGCP3	Q96CW5	939
TUBGCP5	TUBGCP2	Q9BSJ2	922
TUBGCP5	IGFBP2	P18065	915
TUBGCP5	NEDD1	Q8NHV4	871
TUBGCP5	TUBG1	P23258	823
TUBGCP5	MZT1	Q08AG7	820
TUBGCP5	TUBG2	Q9NRH3	690
TUBGCP5	NME7	Q9Y5B8	661
TUBGCP5	ATP10A	O60312	659
TUBGCP5	MAGEL2	Q9UJ55	625

IntAct

73 interactions, top by confidence:

A	B	Type	Score
TUBGCP5	TUBG1	psi-mi:“MI:0914”(association)	0.840
TUBG1	TUBGCP3	psi-mi:“MI:0914”(association)	0.790
MZT2B	TUBG1	psi-mi:“MI:0914”(association)	0.770
TUBG2	TUBGCP3	psi-mi:“MI:0914”(association)	0.640
Mzt2	TUBG1	psi-mi:“MI:0914”(association)	0.560
TUBGCP5	HEMK1	psi-mi:“MI:0915”(physical association)	0.560
LGALS3BP	RGPD8	psi-mi:“MI:0914”(association)	0.530
TUBG2	TXNDC9	psi-mi:“MI:0914”(association)	0.530
MZT1	PCNT	psi-mi:“MI:0914”(association)	0.530
TXNDC12	TUBG1	psi-mi:“MI:0914”(association)	0.530
TUBG2	TCP1	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
PRICKLE3	TUBG1	psi-mi:“MI:0914”(association)	0.530
DNAJB8	DNAJB6	psi-mi:“MI:0914”(association)	0.530
Tubgcp3		psi-mi:“MI:0915”(physical association)	0.400
Mzt2		psi-mi:“MI:0915”(physical association)	0.400
Mzt1		psi-mi:“MI:0915”(physical association)	0.400
Tubg1		psi-mi:“MI:0915”(physical association)	0.400
Tubgcp6		psi-mi:“MI:0915”(physical association)	0.400
Tubg1	BDP1	psi-mi:“MI:0914”(association)	0.350
Nedd1		psi-mi:“MI:0914”(association)	0.350
Tubgcp6	MRE11	psi-mi:“MI:0914”(association)	0.350

BioGRID (106): TUBGCP5 (Affinity Capture-MS), TUBGCP5 (Affinity Capture-MS), CLU (Affinity Capture-MS), ALDH18A1 (Affinity Capture-MS), TUBG1 (Affinity Capture-MS), DNAJC6 (Affinity Capture-MS), TUBGCP3 (Affinity Capture-MS), TUBGCP2 (Affinity Capture-MS), DAPK2 (Affinity Capture-MS), TUBGCP4 (Affinity Capture-MS), NME7 (Affinity Capture-MS), PLEKHG1 (Affinity Capture-MS), MZT2B (Affinity Capture-MS), TUBGCP6 (Affinity Capture-MS), TUBGCP5 (Affinity Capture-MS)

ESM2 similar proteins: A4D1B5, A5PKN5, A7RV13, D3IUT5, O70167, O70173, O75747, P42695, Q12769, Q28HN9, Q3MHH2, Q3TCV3, Q3UPC7, Q3URV1, Q5BKL1, Q5EA76, Q5R8P3, Q5RB52, Q5RC62, Q5RD58, Q5SUD9, Q5ZK21, Q5ZL79, Q63517, Q66H58, Q66HC3, Q66KD9, Q6DFW0, Q6GN08, Q6ZQK0, Q6ZW61, Q8BJW5, Q8BKN5, Q8IV33, Q8K1K4, Q8N957, Q8NB91, Q8R3P6, Q8TAM1, Q91YN0

Diamond homologs: Q8BKN5, Q95K09, Q96RT8

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TUBGCP5	“form complex”	“g-TuRC complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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
Recruitment of mitotic centrosome proteins and complexes	11	37.4×	7e-13
Recruitment of NuMA to mitotic centrosomes	11	32.0×	2e-12
Centrosome maturation	5	31.7×	3e-05
Regulation of PLK1 Activity at G2/M Transition	6	19.0×	3e-05
Mitotic G2-G2/M phases	5	15.9×	5e-04
G2/M Transition	5	15.9×	5e-04
Mitotic Prometaphase	6	10.4×	7e-04
M Phase	6	9.9×	8e-04

GO biological processes:

GO term	Partners	Fold	FDR
microtubule nucleation	8	84.6×	1e-11
cytoplasmic microtubule organization	7	40.8×	6e-08
mitotic cell cycle	8	18.1×	1e-06
microtubule cytoskeleton organization	5	10.3×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	134
Likely benign	13
Benign	28

Top pathogenic / likely-pathogenic (0)

SpliceAI

3813 predictions. Top by Δscore:

Variant	Effect	Δscore
15:23003065:GCG:G	donor_gain	1.0000
15:23003065:GCGG:G	donor_gain	1.0000
15:23003066:GGCG:G	donor_gain	1.0000
15:23003152:G:A	acceptor_loss	1.0000
15:23003153:A:G	acceptor_loss	1.0000
15:23003154:CAG:C	acceptor_loss	1.0000
15:23003155:GCA:G	acceptor_loss	1.0000
15:23003156:TGCAG:T	acceptor_loss	1.0000
15:23003157:CTGCA:C	acceptor_loss	1.0000
15:23004227:A:G	acceptor_gain	1.0000
15:23005430:GG:G	donor_gain	1.0000
15:23005431:GG:G	donor_gain	1.0000
15:23006351:G:GC	acceptor_gain	1.0000
15:23006351:GT:G	acceptor_gain	1.0000
15:23006351:GTCT:G	acceptor_gain	1.0000
15:23006352:A:AG	acceptor_gain	1.0000
15:23011130:G:GG	donor_gain	1.0000
15:23011132:AGGTG:A	donor_loss	1.0000
15:23011133:AAG:A	donor_loss	1.0000
15:23011135:GCAAG:G	donor_gain	1.0000
15:23011330:G:GA	acceptor_gain	1.0000
15:23011330:GA:G	acceptor_gain	1.0000
15:23011330:GAT:G	acceptor_gain	1.0000
15:23011331:A:AG	acceptor_gain	1.0000
15:23011337:T:G	acceptor_gain	1.0000
15:23011337:T:TA	acceptor_gain	1.0000
15:23011338:AT:A	acceptor_gain	1.0000
15:23017773:GAG:G	donor_gain	1.0000
15:23018040:G:GG	acceptor_gain	1.0000
15:23018041:A:AG	acceptor_gain	1.0000

AlphaMissense

6827 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:23004119:A:G	C941R	1.000
15:23004121:C:G	R940P	1.000
15:23004202:A:G	F913S	1.000
15:23004223:A:G	L906P	1.000
15:23006150:A:T	V812D	1.000
15:23008741:A:G	L762P	1.000
15:23017826:A:G	L568P	1.000
15:23017837:C:A	K564N	1.000
15:23017837:C:G	K564N	1.000
15:23017841:C:T	G563D	1.000
15:23018007:A:G	W508R	1.000
15:23018007:A:T	W508R	1.000
15:23019225:A:T	I494N	1.000
15:23019271:A:G	W479R	1.000
15:23019271:A:T	W479R	1.000
15:22999845:A:G	L1017P	0.999
15:22999857:A:G	L1013P	0.999
15:23000576:A:C	F1007L	0.999
15:23000576:A:T	F1007L	0.999
15:23000577:A:G	F1007S	0.999
15:23000578:A:G	F1007L	0.999
15:23000583:C:T	G1005E	0.999
15:23000585:T:A	R1004S	0.999
15:23000585:T:G	R1004S	0.999
15:23000595:G:T	A1001D	0.999
15:23000616:A:G	L994P	0.999
15:23000616:A:T	L994H	0.999
15:23000618:A:C	F993L	0.999
15:23000618:A:T	F993L	0.999
15:23000619:A:G	F993S	0.999

dbSNP variants (sampled 300 via entrez): RS1000178951 (15:23000230 A>G,T), RS1000199392 (15:22995348 G>A,T), RS1000249905 (15:23009590 C>A), RS1000271920 (15:23041363 C>A,T), RS1000337403 (15:22992795 C>T), RS1000384121 (15:23018338 T>C), RS1000432288 (15:22992488 ATATATGTATG>A), RS1000483147 (15:23012531 T>C), RS1000539709 (15:22986442 G>T), RS1000559956 (15:22988347 C>T), RS1000602520 (15:22989428 A>G), RS1000648329 (15:23032389 TTAAA>T), RS1000676660 (15:23020692 A>G), RS1000721619 (15:23034731 C>T), RS1000743623 (15:23006562 T>A,C)

Disease associations

OMIM: gene MIM:608147 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): microcephaly (MONDO:0001149)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000252	Microcephaly

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST007208_14	Obsessive-compulsive disorder	3.000000e-06
GCST009615_16	Triglyceride levels x loop diuretics use interaction	4.000000e-07
GCST009615_17	Triglyceride levels x loop diuretics use interaction	3.000000e-06
GCST012306_11	Bipolar disorder	1.000000e-06
GCST012306_8	Bipolar disorder	3.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008831	Microcephaly	C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Cadmium Chloride	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
bisphenol F	decreases expression, affects cotreatment	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	increases abundance, affects cotreatment, decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Demecolcine	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Vincristine	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05518188	PHASE1/PHASE2	RECRUITING	Melpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT00001639	Not specified	COMPLETED	Evaluation of Patients With Unresolved Chromosome Abnormalities
NCT01151462	Not specified	WITHDRAWN	Postnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
NCT01565005	Not specified	COMPLETED	Microcephaly Genetic Deficiency in Neural Progenitors
NCT02510170	Not specified	COMPLETED	Fetal and Maternal Head Circumference During Pregnancy in Israeli Population
NCT02741882	Not specified	COMPLETED	Zika and Microcephaly: Case-control Study
NCT02943304	Not specified	COMPLETED	Neurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero
NCT03255369	Not specified	UNKNOWN	Vertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF)
NCT03325946	Not specified	RECRUITING	The FBRI VTC Neuromotor Research Clinic
NCT03330600	Not specified	COMPLETED	Efficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome
NCT03548779	Not specified	COMPLETED	North Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
NCT03651687	Not specified	COMPLETED	Guangzhou Surveillance and Clinical Study in Microcephaly (GSCSM)
NCT03922594	Not specified	TERMINATED	Surveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia
NCT04816175	Not specified	COMPLETED	Intensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay
NCT05322980	Not specified	COMPLETED	Summary of Infants Weighing 500 Grams or Less
NCT06019182	Not specified	RECRUITING	MEHMO Natural History and Biomarkers
NCT06566066	Not specified	RECRUITING	Register for Patients With Thyroid Hormone Resistance.