TBX15

Summary

TBX15 (T-box transcription factor 15, HGNC:11594) is a protein-coding gene on chromosome 1p12, encoding T-box transcription factor TBX15 (Q96SF7). Probable transcriptional regulator involved in the development of the skeleton of the limb, vertebral column and head.

This gene belongs to the T-box family of genes, which encode a phylogenetically conserved family of transcription factors that regulate a variety of developmental processes. All these genes contain a common T-box DNA-binding domain. Mutations in this gene are associated with Cousin syndrome.

Source: NCBI Gene 6913 — RefSeq curated summary.

At a glance

• Gene–disease (curated): pelviscapular dysplasia (Definitive, GenCC)
• GWAS associations: 222
• Clinical variants (ClinVar): 246 total — 3 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 63
• Transcription factor: yes — 29 downstream targets (CollecTRI)
• MANE Select transcript: NM_001330677

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11594
Approved symbol	TBX15
Name	T-box transcription factor 15
Location	1p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000092607
Ensembl biotype	protein_coding
OMIM	604127
Entrez	6913

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000207157, ENST00000369429, ENST00000449873

RefSeq mRNA: 2 — MANE Select: NM_001330677 NM_001330677, NM_152380

CCDS: CCDS30816, CCDS81360

Canonical transcript exons

ENST00000369429 — 8 exons

Exon	Start	End
ENSE00000957921	118899028	118899125
ENSE00001450018	118987591	118988343
ENSE00001641386	118924646	118924817
ENSE00001650281	118923436	118923603
ENSE00001714968	118914115	118914179
ENSE00001719934	118883047	118885516
ENSE00001770754	118926510	118926611
ENSE00003508985	118931619	118931832

Expression profiles

Bgee: expression breadth ubiquitous, 172 present calls, max score 96.63.

FANTOM5 (CAGE): breadth broad, TPM avg 5.0089 / max 864.4172, expressed in 603 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
14056	2.9915	337
14050	0.9793	412
14051	0.3693	189
14053	0.2490	130
14055	0.1990	92
14057	0.0842	41
14054	0.0591	28
14052	0.0570	14
14047	0.0204	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	96.63	gold quality
muscle of leg	UBERON:0001383	96.47	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.11	gold quality
quadriceps femoris	UBERON:0001377	96.06	gold quality
vastus lateralis	UBERON:0001379	96.02	gold quality
tibialis anterior	UBERON:0001385	95.43	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.33	gold quality
skeletal muscle tissue	UBERON:0001134	94.40	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.20	gold quality
biceps brachii	UBERON:0001507	93.93	gold quality
tibia	UBERON:0000979	93.37	gold quality
deltoid	UBERON:0001476	92.31	gold quality
calcaneal tendon	UBERON:0003701	91.54	gold quality
tendon	UBERON:0000043	91.50	gold quality
cartilage tissue	UBERON:0002418	90.84	gold quality
popliteal artery	UBERON:0002250	90.47	gold quality
tibial artery	UBERON:0007610	90.47	gold quality
tendon of biceps brachii	UBERON:0008188	90.41	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.58	gold quality
muscle tissue	UBERON:0002385	88.58	gold quality
nerve	UBERON:0001021	83.42	gold quality
tibial nerve	UBERON:0001323	83.42	gold quality
liver	UBERON:0002107	82.08	gold quality
adipose tissue	UBERON:0001013	80.92	gold quality
thoracic mammary gland	UBERON:0005200	80.70	gold quality
mammary gland	UBERON:0001911	80.68	gold quality
layer of synovial tissue	UBERON:0007616	80.58	gold quality
right lobe of liver	UBERON:0001114	80.38	gold quality
body of tongue	UBERON:0011876	79.49	gold quality
skin of leg	UBERON:0001511	79.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.87

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

29 targets.

Target	Regulation
BGLAP
CD44
COL2A1
DLD
DNASE2B
DOT1L
EGFR
ESR2
FADD
GJA1
HTR1A
IGF1R
KL
LHCGR
MSI1
PLIN2
PSMD10
RASSF1
RB1
SCNN1A
SENP2
SERPINA1
SMC3
TBX15
TBX2
TERT
TFAP2A
TP53
TRIM28

JASPAR motifs

Motif	Name	Family
MA0803.1	TBX15	TBX1-related factors

JASPAR matrix evidence (PMIDs): PMID:12093383

Upstream regulators (CollecTRI, top): PDX1, TBX15

miRNA regulators (miRDB)

88 targeting TBX15, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209

Literature-anchored findings (GeneRIF, showing 17)

• TBX15 mutations cause craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature in Cousin syndrome. (PMID:19068278)
• TBX15 might be involved in the pathophysiology of placental diseases. (PMID:20962579)
• Genes within recently identified loci associated with waist-hip ratio (WHR) exhibit fat depot-specific mRNA expression, which correlates with obesity-related traits. Adipose tissue (AT) mRNA expression of 6 genes (TBX15/WARS2, STAB1, PIGC, ZNRF3, GRB14 (PMID:23670221)
• We identified homozygosity for a novel nonsense mutation (c.841C>T) in TBX15 predicted to cause a premature stop (p.Arg281*) with truncation of the protein. (PMID:24039145)
• Two traits of ear pinna anatomic variation are associated with SNPs in a region overlapping the TBX15 gene. (PMID:26105758)
• The results indicate the antiapoptotic role of TBX15 in cancer cells, suggesting a contribution of TBX15 in carcinogenesis. (PMID:26216026)
• TBX15 and NF-kappaB found in this study may be important to understand cancer and development processes. (PMID:27327083)
• first genome-wide scan for selection in Inuit from Greenland. A region, with a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome contains two genes, WARS2 and TBX15. our study suggests a complex multi-factorial regulation of TBX15 and WARS2. We show that the introgressed region is associated with regional changes in methylation and expression levels (PMID:28007980)
• These studies showed that Tbx15 differentially regulates oxidative and glycolytic metabolism within subpopulations of white adipocytes and preadipocytes. (PMID:28847884)
• Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15. (PMID:31975641)
• CircPVT1 promotes progression in clear cell renal cell carcinoma by sponging miR-145-5p and regulating TBX15 expression. (PMID:33453148)
• TBX15 rs98422, DNM3 rs1011731, RAD51B rs8017304, and rs2588809 Gene Polymorphisms and Associations With Pituitary Adenoma. (PMID:33622874)
• Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes. (PMID:34340684)
• Harnessing tissue-specific genetic variation to dissect putative causal pathways between body mass index and cardiometabolic phenotypes. (PMID:35090585)
• Mutations in the TBX15-ADAMTS2 pathway associate with a novel soft palate dysplasia. (PMID:36124393)
• miR-4732-3p prevents lung cancer progression via inhibition of the TBX15/TNFSF11 axis. (PMID:37125501)
• The overexpression and clinical significance of TBX15 in human gliomas. (PMID:37328486)

Cross-species orthologs

14 orthologs

Organism	Symbol	Gene ID
danio_rerio	tbx15	ENSDARG00000002582
mus_musculus	Tbx15	ENSMUSG00000027868
rattus_norvegicus	Tbx15	ENSRNOG00000019565
drosophila_melanogaster	H15	FBGN0016660
drosophila_melanogaster	mid	FBGN0261963
drosophila_melanogaster	ocm	FBGN0266083
caenorhabditis_elegans		WBGENE00003106
caenorhabditis_elegans		WBGENE00004750
caenorhabditis_elegans		WBGENE00006545
caenorhabditis_elegans		WBGENE00006546
caenorhabditis_elegans		WBGENE00006556
caenorhabditis_elegans		WBGENE00006557
caenorhabditis_elegans		WBGENE00006559
caenorhabditis_elegans		WBGENE00044798

Paralogs (16): TBX21 (ENSG00000073861), TBX5 (ENSG00000089225), TBX18 (ENSG00000112837), TBX2 (ENSG00000121068), TBX4 (ENSG00000121075), TBX22 (ENSG00000122145), TBX3 (ENSG00000135111), TBR1 (ENSG00000136535), TBX19 (ENSG00000143178), TBX6 (ENSG00000149922), EOMES (ENSG00000163508), TBXT (ENSG00000164458), TBX20 (ENSG00000164532), TBX10 (ENSG00000167800), MGA (ENSG00000174197), TBX1 (ENSG00000184058)

Protein

Protein identifiers

T-box transcription factor TBX15 — Q96SF7 (reviewed: Q96SF7)

Alternative names: T-box transcription factor TBX14

All UniProt accessions (2): Q96SF7, Q5JT55

UniProt curated annotations — full annotation on UniProt →

Function. Probable transcriptional regulator involved in the development of the skeleton of the limb, vertebral column and head. Acts by controlling the number of mesenchymal precursor cells and chondrocytes.

Subunit / interactions. Can form a heterodimer with TBX18.

Subcellular location. Nucleus.

Disease relevance. Cousin syndrome (COUSS) [MIM:260660] Defined as pelviscapular dysplasia with epiphyseal abnormalities, congenital dwarfism and facial dysmorphy (frontal bossing, hypertelorism, narrow palpebral fissures, deep set globes, strabismus, low-set posteriory rotated and unusually formed external ears, dysplasia of conchae, small chin, short neck with redundant skin folds, and a low hairline). Intelligence may vary from normal to moderately impaired. Radiographic features comprise aplasia of the body of the scapula, hypoplasia of the iliac bone, humeroradial synosthosis, dislocation of the femoral heads, and moderate brachydactyly. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Gene prediction based on similarity to orthologs.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96SF7-1	1	yes
Q96SF7-2	2

RefSeq proteins (2): NP_001317606, NP_689593 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001699	TF_T-box	Family
IPR008967	p53-like_TF_DNA-bd_sf	Homologous_superfamily
IPR018186	TF_T-box_CS	Conserved_site
IPR036960	T-box_sf	Homologous_superfamily
IPR046360	T-box_DNA-bd	Domain

Pfam: PF00907

UniProt features (11 total): region of interest 3, compositionally biased region 3, chain 1, DNA-binding region 1, sequence variant 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96SF7-F1	61.41	0.31

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 (1): 330

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 278 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS, GOBP_CRANIAL_SKELETAL_SYSTEM_DEVELOPMENT, chr1p12, GOBP_EMBRYO_DEVELOPMENT, GOBP_CELL_FATE_SPECIFICATION, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_CELL_FATE_COMMITMENT, GOBP_EMBRYONIC_ORGAN_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_EMBRYONIC_CRANIAL_SKELETON_MORPHOGENESIS

GO Biological Process (7): cell fate specification (GO:0001708), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of DNA-templated transcription (GO:0045893), embryonic cranial skeleton morphogenesis (GO:0048701), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355), embryonic skeletal system morphogenesis (GO:0048704)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), protein homodimerization activity (GO:0042803), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), RNA polymerase II transcription repressor complex (GO:0090571)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
transcription by RNA polymerase II	2
DNA-templated transcription	2
regulation of transcription by RNA polymerase II	2
cell fate commitment	1
cellular developmental process	1
positive regulation of RNA biosynthetic process	1
embryonic skeletal system morphogenesis	1
cranial skeletal system development	1
negative regulation of DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
embryonic organ morphogenesis	1
skeletal system morphogenesis	1
embryonic skeletal system development	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
identical protein binding	1
protein dimerization activity	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1
transcription repressor complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

1150 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TBX15	WARS2	Q9UGM6	737
TBX15	TLE3	Q04726	670
TBX15	SHOX2	O60902	532
TBX15	ALX3	O95076	522
TBX15	BNC2	Q6ZN30	498
TBX15	HOXC9	P31274	470
TBX15	WDR3	Q9UNX4	445
TBX15	KCNH7	Q9NS40	443
TBX15	OCA2	Q04671	435
TBX15	HOXD3	P31249	429
TBX15	GDAP2	Q9NXN4	427
TBX15	HOXA5	P20719	424
TBX15	GPC4	O75487	424
TBX15	PAX1	P15863	419
TBX15	HOXC13	P31276	417
TBX15	HOXC10	Q9NYD6	417

IntAct

40 interactions, top by confidence:

A	B	Type	Score
TBX15	VENTX	psi-mi:“MI:0915”(physical association)	0.670
VENTX	TBX15	psi-mi:“MI:0915”(physical association)	0.670
TBX15	ATXN1	psi-mi:“MI:0915”(physical association)	0.560
POLE2	TBX15	psi-mi:“MI:0915”(physical association)	0.560
ATXN1	TBX15	psi-mi:“MI:0915”(physical association)	0.560
TBX15	POLE2	psi-mi:“MI:0915”(physical association)	0.560
TBX6	TBX15	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	TBX15	psi-mi:“MI:0915”(physical association)	0.560
MYOZ3	TBX15	psi-mi:“MI:0915”(physical association)	0.560
DOK6	TBX15	psi-mi:“MI:0915”(physical association)	0.560
RHOBTB3	TBX15	psi-mi:“MI:0915”(physical association)	0.560
TEKT5	TBX15	psi-mi:“MI:0915”(physical association)	0.560
VGLL3	TBX15	psi-mi:“MI:0915”(physical association)	0.560
DTX2	TBX15	psi-mi:“MI:0915”(physical association)	0.560
HOXA1	TBX15	psi-mi:“MI:0915”(physical association)	0.560
DLG1	TBX15	psi-mi:“MI:0915”(physical association)	0.400
TBX15	TBX15	psi-mi:“MI:0915”(physical association)	0.370
TBX6	TBX15	psi-mi:“MI:0915”(physical association)	0.000
VGLL3	TBX15	psi-mi:“MI:0915”(physical association)	0.000
DTX2	TBX15	psi-mi:“MI:0915”(physical association)	0.000
HOXA1	TBX15	psi-mi:“MI:0915”(physical association)	0.000
NTAQ1	TBX15	psi-mi:“MI:0915”(physical association)	0.000
MYOZ3	TBX15	psi-mi:“MI:0915”(physical association)	0.000
DOK6	TBX15	psi-mi:“MI:0915”(physical association)	0.000
RHOBTB3	TBX15	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): TBX15 (Two-hybrid), TBX15 (Two-hybrid), TBX15 (Two-hybrid), VENTX (Two-hybrid), TBX15 (Two-hybrid), HOXA1 (Two-hybrid), TBX6 (Two-hybrid), TEKT5 (Two-hybrid), WDYHV1 (Two-hybrid), RHOBTB3 (Two-hybrid), MYOZ3 (Two-hybrid), DOK6 (Two-hybrid), VGLL3 (Two-hybrid), TBX15 (Proximity Label-MS)

ESM2 similar proteins: A1L2P5, A8WFJ9, B7ZS42, O01409, O13606, O42261, O42370, O70306, O74412, P09013, P09089, P22199, P24781, P33205, P49844, P56158, P70056, P79742, P79777, P80492, Q03414, Q07998, Q17134, Q1LXZ9, Q25113, Q3SA47, Q3YC04, Q5J3Q5, Q5R9P5, Q6DIB4, Q6NVT7, Q6P8A3, Q7ZYQ0, Q8AXX2, Q8BUR3, Q8JIT5, Q8K402, Q91661, Q91904, Q91905

Diamond homologs: A1YF56, A2AWL7, D3ZJK7, E1BEA8, O01409, O13161, O15119, O15178, O17212, O43435, O54839, O60806, O70306, O73718, O75333, O95935, O95936, O95947, P20293, P24781, P55965, P56158, P57082, P70323, P70324, P70325, P70326, P70327, P79742, P79777, P79778, P79779, P79944, P80492, P87377, P90971, Q07998, Q13207, Q16650, Q17134

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	110
Likely benign	81
Benign	40

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
1073859	NM_001330677.2(TBX15):c.883C>T (p.Arg295Ter)	Pathogenic
5822	NM_001330677.2(TBX15):c.1348del (p.Ile450fs)	Pathogenic
5823	NM_001330677.2(TBX15):c.1350del (p.Pro451fs)	Pathogenic
806196	NM_001330677.2(TBX15):c.990del (p.Phe331fs)	Likely pathogenic

SpliceAI

2208 predictions. Top by Δscore:

Variant	Effect	Δscore
1:118899022:CTTTA:C	donor_loss	1.0000
1:118899023:TTTAC:T	donor_loss	1.0000
1:118899024:TTA:T	donor_loss	1.0000
1:118899025:TACCT:T	donor_loss	1.0000
1:118899026:ACCTT:A	donor_loss	1.0000
1:118899027:CCTTG:C	donor_gain	1.0000
1:118899126:C:CC	acceptor_gain	1.0000
1:118923430:TCTTA:T	donor_loss	1.0000
1:118923431:CTTAC:C	donor_loss	1.0000
1:118923432:TTAC:T	donor_loss	1.0000
1:118923433:TACC:T	donor_loss	1.0000
1:118923435:CCTG:C	donor_gain	1.0000
1:118923600:TGAT:T	acceptor_gain	1.0000
1:118931613:CCTTA:C	donor_loss	1.0000
1:118931614:CTTA:C	donor_loss	1.0000
1:118931615:TTA:T	donor_loss	1.0000
1:118931618:C:CA	donor_loss	1.0000
1:118931618:CCTG:C	donor_gain	1.0000
1:118896799:T:C	acceptor_gain	0.9900
1:118899121:CAGTT:C	acceptor_gain	0.9900
1:118899123:GTT:G	acceptor_gain	0.9900
1:118899124:TT:T	acceptor_gain	0.9900
1:118899125:TC:T	acceptor_loss	0.9900
1:118899126:CTGAC:C	acceptor_loss	0.9900
1:118899143:A:T	acceptor_gain	0.9900
1:118900259:T:TA	donor_gain	0.9900
1:118923434:A:AC	donor_gain	0.9900
1:118923435:C:CC	donor_gain	0.9900
1:118923599:ATGAT:A	acceptor_gain	0.9900
1:118923601:GAT:G	acceptor_gain	0.9900

AlphaMissense

3960 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:118914131:C:G	D304H	1.000
1:118914132:T:A	R303S	1.000
1:118914132:T:G	R303S	1.000
1:118914133:C:A	R303I	1.000
1:118914133:C:G	R303T	1.000
1:118914134:T:C	R303G	1.000
1:118914135:G:C	F302L	1.000
1:118914135:G:T	F302L	1.000
1:118914136:A:C	F302C	1.000
1:118914136:A:G	F302S	1.000
1:118914137:A:C	F302V	1.000
1:118914137:A:G	F302L	1.000
1:118914137:A:T	F302I	1.000
1:118914139:C:A	G301V	1.000
1:118914139:C:T	G301E	1.000
1:118914140:C:G	G301R	1.000
1:118914140:C:T	G301R	1.000
1:118914141:T:A	K300N	1.000
1:118914141:T:G	K300N	1.000
1:118914142:T:A	K300I	1.000
1:118914142:T:G	K300T	1.000
1:118914143:T:C	K300E	1.000
1:118914143:T:G	K300Q	1.000
1:118914145:G:A	A299V	1.000
1:118914145:G:C	A299G	1.000
1:118914145:G:T	A299D	1.000
1:118914146:C:G	A299P	1.000
1:118914146:C:T	A299T	1.000
1:118914147:A:C	F298L	1.000
1:118914147:A:T	F298L	1.000

dbSNP variants (sampled 300 via entrez): RS1000026876 (1:118989461 CG>C), RS1000057534 (1:118948406 CA>C,CAA), RS1000065747 (1:118905573 C>A,T), RS1000093146 (1:118987935 T>G), RS1000108141 (1:118987273 C>T), RS1000112696 (1:118988617 C>A,G,T), RS1000121990 (1:118945408 T>C), RS1000123904 (1:118946736 A>G), RS1000131582 (1:118955176 G>A), RS1000147305 (1:118945056 C>G), RS1000149776 (1:118902792 C>T), RS1000176188 (1:118887098 G>T), RS1000288072 (1:118886886 C>T), RS1000302727 (1:118928235 T>C), RS1000337940 (1:118934405 G>A,C)

Disease associations

OMIM: gene MIM:604127 | disease phenotypes: MIM:260660

GenCC curated gene-disease

Disease	Classification	Inheritance
pelviscapular dysplasia	Definitive	Autosomal recessive

Mondo (1): pelviscapular dysplasia (MONDO:0009845)

Orphanet (1): Pelviscapular dysplasia (Orphanet:93333)

HPO phenotypes

63 total (30 of 63 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000033	Ambiguous genitalia, male
HP:0000061	Ambiguous genitalia, female
HP:0000126	Hydronephrosis
HP:0000171	Microglossia
HP:0000175	Cleft palate
HP:0000238	Hydrocephalus
HP:0000256	Macrocephaly
HP:0000294	Low anterior hairline
HP:0000316	Hypertelorism
HP:0000347	Micrognathia
HP:0000358	Posteriorly rotated ears
HP:0000365	Hearing impairment
HP:0000369	Low-set ears
HP:0000377	Abnormal pinna morphology
HP:0000402	Stenosis of the external auditory canal
HP:0000470	Short neck
HP:0000482	Microcornea
HP:0000486	Strabismus
HP:0000490	Deeply set eye
HP:0000568	Microphthalmia
HP:0000581	Blepharophimosis
HP:0000882	Hypoplastic scapulae
HP:0000890	Long clavicles
HP:0000946	Hypoplastic ilia
HP:0001156	Brachydactyly
HP:0001239	Wrist flexion contracture
HP:0001374	Congenital hip dislocation
HP:0001591	Bell-shaped thorax
HP:0001762	Talipes equinovarus

GWAS associations

222 associations (top):

Study	Trait	p-value
GCST000829_3	Waist-hip ratio	9.000000e-25
GCST002036_1	Congenital heart malformation	8.000000e-10
GCST002782_1	Waist-to-hip ratio adjusted for body mass index	1.000000e-07
GCST002782_104	Waist-to-hip ratio adjusted for body mass index	7.000000e-06
GCST002782_105	Waist-to-hip ratio adjusted for body mass index	8.000000e-09
GCST002782_106	Waist-to-hip ratio adjusted for body mass index	7.000000e-06
GCST002782_107	Waist-to-hip ratio adjusted for body mass index	4.000000e-09
GCST002782_2	Waist-to-hip ratio adjusted for body mass index	2.000000e-19
GCST002782_211	Waist-to-hip ratio adjusted for body mass index	2.000000e-14
GCST002782_3	Waist-to-hip ratio adjusted for body mass index	7.000000e-08
GCST002782_4	Waist-to-hip ratio adjusted for body mass index	7.000000e-15
GCST002782_5	Waist-to-hip ratio adjusted for body mass index	2.000000e-20
GCST002782_90	Waist-to-hip ratio adjusted for body mass index	3.000000e-12
GCST002782_91	Waist-to-hip ratio adjusted for body mass index	5.000000e-09
GCST002782_92	Waist-to-hip ratio adjusted for body mass index	2.000000e-18
GCST002782_93	Waist-to-hip ratio adjusted for body mass index	6.000000e-09
GCST002782_94	Waist-to-hip ratio adjusted for body mass index	3.000000e-13
GCST002782_95	Waist-to-hip ratio adjusted for body mass index	2.000000e-19
GCST002783_578	Body mass index	7.000000e-07
GCST002996_1	Folding of antihelix	1.000000e-11
GCST003001_1	Ear morphology	5.000000e-12
GCST003003_1	Antitragus size	2.000000e-08
GCST003338_5	Waist-to-hip ratio adjusted for body mass index	4.000000e-06
GCST003983_15	Male-pattern baldness	9.000000e-14
GCST003985_12	Breast size	4.000000e-09
GCST003985_15	Breast size	1.000000e-07
GCST003989_25	Chin dimples	2.000000e-13
GCST004063_79	Waist circumference adjusted for body mass index	1.000000e-12
GCST004063_81	Waist circumference adjusted for body mass index	1.000000e-24
GCST004063_82	Waist circumference adjusted for body mass index	2.000000e-15

EFO canonical traits (17, from GWAS)

EFO ID	Trait name
EFO:0004343	waist-hip ratio
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0004340	body mass index
EFO:0007671	folding of antihelix
EFO:0007664	outer ear morphology trait
EFO:0007669	antitragus size
EFO:0007789	BMI-adjusted waist circumference
EFO:0004312	vital capacity
EFO:0004318	smoking behavior
EFO:0008002	physical activity measurement
EFO:0009270	heel bone mineral density
EFO:0004344	birth weight
EFO:0004314	forced expiratory volume
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0008039	BMI-adjusted hip circumference
EFO:0008343	sex interaction measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C535550	Pelviscapular dysplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	3
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Aflatoxin B1	decreases methylation, increases expression	2
pirinixic acid	affects binding, increases activity, increases expression	1
arsenite	increases methylation	1
sulforaphane	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, decreases expression	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
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Vorinostat	increases expression, affects cotreatment	1
Calcitriol	increases expression, affects cotreatment	1
Cisplatin	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Gallic Acid	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Methyl Methanesulfonate	increases expression	1
N-Nitrosopyrrolidine	increases expression	1
Nickel	decreases expression	1
Potassium Dichromate	increases expression	1
Dihydrotestosterone	increases expression	1
Testosterone	affects cotreatment, increases expression, decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Gold Compounds	decreases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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