GSC

Summary

GSC (goosecoid homeobox, HGNC:4612) is a protein-coding gene on chromosome 14q32.13, encoding Homeobox protein goosecoid (P56915). Regulates chordin (CHRD).

This gene encodes a member of the bicoid subfamily of the paired (PRD) homeobox family of proteins. The encoded protein acts as a transcription factor and may be autoregulatory. A similar protein in mice plays a role in craniofacial and rib cage development during embryogenesis.

Source: NCBI Gene 145258 — RefSeq curated summary.

At a glance

• Gene–disease (curated): short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome (Strong, GenCC)
• GWAS associations: 4
• Clinical variants (ClinVar): 120 total — 3 pathogenic
• Phenotypes (HPO): 32
• Transcription factor: yes — 16 downstream targets (CollecTRI)
• MANE Select transcript: NM_173849

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4612
Approved symbol	GSC
Name	goosecoid homeobox
Location	14q32.13
Locus type	gene with protein product
Status	Approved
Aliases	GSC1
Ensembl gene	ENSG00000133937
Ensembl biotype	protein_coding
OMIM	138890
Entrez	145258

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000238558

RefSeq mRNA: 1 — MANE Select: NM_173849 NM_173849

CCDS: CCDS9930

Canonical transcript exons

ENST00000238558 — 3 exons

Exon	Start	End
ENSE00001011272	94768958	94769217
ENSE00001302494	94769661	94770113
ENSE00001306055	94768223	94768649

Expression profiles

Bgee: expression breadth broad, 98 present calls, max score 92.63.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7398 / max 27.0525, expressed in 308 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
144758	0.7398	308

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.63	gold quality
calcaneal tendon	UBERON:0003701	91.33	gold quality
tendon	UBERON:0000043	73.85	gold quality
hindlimb stylopod muscle	UBERON:0004252	65.18	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	65.17	gold quality
subcutaneous adipose tissue	UBERON:0002190	65.10	gold quality
omental fat pad	UBERON:0010414	64.97	gold quality
peritoneum	UBERON:0002358	64.90	gold quality
adipose tissue of abdominal region	UBERON:0007808	63.64	gold quality
gastrocnemius	UBERON:0001388	61.92	gold quality
muscle of leg	UBERON:0001383	61.84	gold quality
right lobe of thyroid gland	UBERON:0001119	61.76	gold quality
adipose tissue	UBERON:0001013	59.44	gold quality
left lobe of thyroid gland	UBERON:0001120	58.61	gold quality
apex of heart	UBERON:0002098	58.41	gold quality
thyroid gland	UBERON:0002046	57.76	gold quality
granulocyte	CL:0000094	57.13	gold quality
tibial nerve	UBERON:0001323	56.07	gold quality
tibial artery	UBERON:0007610	55.21	gold quality
popliteal artery	UBERON:0002250	55.09	gold quality
skin of abdomen	UBERON:0001416	54.35	gold quality
parotid gland	UBERON:0001831	53.69	gold quality
nasal cavity mucosa	UBERON:0001826	52.46	gold quality
skin of leg	UBERON:0001511	52.33	gold quality
aorta	UBERON:0000947	51.99	gold quality
zone of skin	UBERON:0000014	51.30	gold quality
lymph node	UBERON:0000029	51.19	gold quality
saliva-secreting gland	UBERON:0001044	50.99	gold quality
minor salivary gland	UBERON:0001830	50.72	gold quality
mouth mucosa	UBERON:0003729	49.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.46

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

16 targets.

Target	Regulation
ADAM2
BMP4
CDH5
CHRD	Unknown
EPHA7	Repression
EVX1	Repression
FOXC2	Activation
FOXH1
GSC	Repression
GSC2	Unknown
GTF2I
IGKC
INHBA
MIXL1
PAX3
PROM1

JASPAR motifs

Motif	Name	Family
MA0648.1	GSC	Paired-related HD factors
MA0648.2	GSC	Paired-related HD factors
MA2629.1	GSC::TBX21	Paired-related HD factors::TBX1-related factors

JASPAR matrix evidence (PMIDs): PMID:18585359, PMID:20211142

Upstream regulators (CollecTRI, top): DLX5, EVX1, FOXH1, GSC, GTF2I, HHEX, JUN, LHX8, MIXL1, OTX2, PAX3, PITX2, SMAD2, SMAD3, SMAD4, TBXT

miRNA regulators (miRDB)

15 targeting GSC, 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-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-6884-3P	98.05	65.32	750
HSA-MIR-562	97.66	65.63	698
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-885-3P	95.14	63.08	448
HSA-MIR-6879-3P	93.93	64.00	759
HSA-MIR-4444	92.67	67.92	56

Literature-anchored findings (GeneRIF, showing 14)

• Goosecoid promotes tumor cell malignancy and suggest that other conserved organizer genes may function similarly in human cancer (PMID:17142318)
• GSC protein might contribute to the observed phenotype. (PMID:18074379)
• The goosecoid gene mutation in exon 3 may be involved in the malformation events (microtia) in this family. (PMID:20195123)
• the 4 recently reported SNPs,located near BNC2, SORCS1, GSC and WDR72 loci, affecting glycemic control in type 1 diabetes had no apparent effect on HbA1c in type 2 diabetes; but, for SORCS1 SNP, findings do not rule out possible relationship with HbA1c (PMID:21294870)
• GSC represses EVX1 expression and is required for development of anterior primitive-streak-like cell progeny in response to activin. (PMID:22178155)
• EtOH exposure increased the expression of an organizer specific gene, goosecoid, in human embryonic carcinoma cells. (PMID:23378141)
• SAMS, a syndrome of short stature, auditory-canal atresia, mandibular hypoplasia, and skeletal abnormalities is a unique neurocristopathy caused by mutations in Goosecoid. (PMID:24290375)
• Results suggest that GSC is the most potential biomarker of drug response and poor prognosis in ovarian serous carcinomas. (PMID:24858567)
• GSC is also a prognostic factor for poor survival and metastasis of HCC, which suggests its potential as a therapeutic target for metastatic HCC. (PMID:25343336)
• Performed mutational analysis of TCOF1, GSC, and HOXA2 to determine the mutational features of the 3 genes in Chinese patients with Treacher Collins syndrome. (PMID:27526242)
• We find that DIGIT is divergent to Goosecoid (GSC) and expressed during endoderm differentiation. Deletion of the SMAD3-occupied enhancer proximal to DIGIT inhibits DIGIT and GSC expression and definitive endoderm differentiation. (PMID:27705785)
• 5 genomic variants in GSC, HOXA2 and PRKRA were identified through mutational analysis in Chinese patients with microtia. (PMID:28109504)
• USP21 modulates Goosecoid function through deubiquitination. (PMID:31253698)
• Goosecoid promotes pancreatic adenocarcinoma metastasis through TGF-beta signaling. (PMID:39097890)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	gsc	ENSDARG00000059073
mus_musculus	Gsc	ENSMUSG00000021095
rattus_norvegicus	Gsc	ENSRNOG00000010605

Paralogs (50): ARX (ENSG00000004848), PAX6 (ENSG00000007372), PAX7 (ENSG00000009709), ALX4 (ENSG00000052850), GSC2 (ENSG00000063515), PITX1 (ENSG00000069011), PAX2 (ENSG00000075891), RHOXF1 (ENSG00000101883), CRX (ENSG00000105392), EVX1 (ENSG00000106038), PAX4 (ENSG00000106331), NOBOX (ENSG00000106410), PITX3 (ENSG00000107859), PHOX2B (ENSG00000109132), OTX1 (ENSG00000115507), PRRX1 (ENSG00000116132), VSX2 (ENSG00000119614), ESX1 (ENSG00000123576), PAX8 (ENSG00000125618), PAX1 (ENSG00000125813), RHOXF2 (ENSG00000131721), RAX (ENSG00000134438), PAX3 (ENSG00000135903), ALX3 (ENSG00000156150), HESX1 (ENSG00000163666), PITX2 (ENSG00000164093), UNCX (ENSG00000164853), PHOX2A (ENSG00000165462), OTX2 (ENSG00000165588), DRGX (ENSG00000165606), PRRX2 (ENSG00000167157), SHOX2 (ENSG00000168779), OTP (ENSG00000171540), RAX2 (ENSG00000173976), EVX2 (ENSG00000174279), PROP1 (ENSG00000175325), ISX (ENSG00000175329), ALX1 (ENSG00000180318), MIXL1 (ENSG00000185155), SHOX (ENSG00000185960)

Protein

Protein identifiers

Homeobox protein goosecoid — P56915 (reviewed: P56915)

All UniProt accessions (1): P56915

UniProt curated annotations — full annotation on UniProt →

Function. Regulates chordin (CHRD). May play a role in spatial programing within discrete embryonic fields or lineage compartments during organogenesis. In concert with NKX3-2, plays a role in defining the structural components of the middle ear; required for the development of the entire tympanic ring. Probably involved in the regulatory networks that define neural crest cell fate specification and determine mesoderm cell lineages in mammals.

Subcellular location. Nucleus.

Disease relevance. Short stature, auditory canal atresia, mandibular hypoplasia, skeletal abnormalities (SAMS) [MIM:602471] An autosomal recessive developmental disorder with features of a first and second branchial arch syndrome, and with unique rhizomelic skeletal anomalies. Craniofacial abnormalities can lead to conductive hearing loss, respiratory insufficiency, and feeding difficulties. Skeletal features include bilateral humeral hypoplasia, humeroscapular synostosis, pelvic abnormalities, and proximal defects of the femora. Affected individuals may also have some features of a neurocristopathy or abnormal mesoderm development, such as urogenital anomalies, that are distinct from other branchial arch syndromes. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the paired homeobox family. Bicoid subfamily.

RefSeq proteins (1): NP_776248* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR051440	Goosecoid-like_HB	Family

Pfam: PF00046

UniProt features (11 total): sequence conflict 4, helix 3, chain 1, DNA-binding region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2DMU	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P56915-F1	65.68	0.23

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-9754189	Germ layer formation at gastrulation
R-HSA-9823730	Formation of definitive endoderm
R-HSA-2892245	POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation

MSigDB gene sets: 255 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_NEURAL_TUBE_DEVELOPMENT, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, LHX3_01, GOBP_DORSAL_VENTRAL_PATTERN_FORMATION, SP1_Q2_01, GOBP_FOREBRAIN_DEVELOPMENT, IRF7_01, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, YGACNNYACAR_UNKNOWN

GO Biological Process (17): regulation of transcription by RNA polymerase II (GO:0006357), gastrulation (GO:0007369), neural crest cell fate specification (GO:0014036), Wnt signaling pathway (GO:0016055), dorsal/ventral neural tube patterning (GO:0021904), signal transduction involved in regulation of gene expression (GO:0023019), negative regulation of Wnt signaling pathway (GO:0030178), forebrain development (GO:0030900), middle ear morphogenesis (GO:0042474), muscle organ morphogenesis (GO:0048644), embryonic skeletal system morphogenesis (GO:0048704), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355), anatomical structure morphogenesis (GO:0009653), tissue development (GO:0009888), ear development (GO:0043583), animal organ development (GO:0048513)

GO Molecular Function (6): 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), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), transcription regulator complex (GO:0005667)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Gastrulation	2
Transcriptional regulation of pluripotent stem cells	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anatomical structure development	4
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
transcription by RNA polymerase II	2
embryonic morphogenesis	2
regulation of gene expression	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
ectoderm formation	1
endoderm formation	1
mesoderm formation	1
neural crest cell fate commitment	1
stem cell fate specification	1
cell surface receptor signaling pathway	1
dorsal/ventral pattern formation	1
neural tube patterning	1
signal transduction	1
negative regulation of signal transduction	1
Wnt signaling pathway	1
regulation of Wnt signaling pathway	1
brain development	1
ear morphogenesis	1
muscle organ development	1
animal organ morphogenesis	1
embryonic organ morphogenesis	1
skeletal system morphogenesis	1
embryonic skeletal system development	1
negative regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of RNA biosynthetic process	1
developmental process	1
sensory organ 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
DNA-binding transcription factor binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1

Protein interactions and networks

STRING

458 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GSC	NODAL	Q96S42	479
GSC	TVP23A	A6NH52	451
GSC	FMO5	P49326	437
GSC	FOXC2	Q99958	399
GSC	EPHX4	Q8IUS5	388
GSC	FAM228A	Q86W67	370
GSC	FBXL17	Q9UF56	367
GSC	NEXMIF	Q5QGS0	360
GSC	CHRD	Q9H2X0	352
GSC	CACNA1I	Q9P0X4	352
GSC	SOX17	Q9H6I2	348
GSC	NHLH1	Q02575	347
GSC	COP1	Q8NHY2	342
GSC	REELD1	A0A1B0GV85	326
GSC	SNAI2	O43623	322

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GSC	DSG4	psi-mi:“MI:0914”(association)	0.350
GSC	DUSP14	psi-mi:“MI:0914”(association)	0.350

BioGRID (81): LRRC15 (Affinity Capture-MS), DSG4 (Affinity Capture-MS), FOXA2 (Reconstituted Complex), GSC (Affinity Capture-Western), DSG4 (Affinity Capture-MS), LRRC15 (Affinity Capture-MS), IAH1 (Affinity Capture-MS), DUSP14 (Affinity Capture-MS), GSC (Positive Genetic), TBX3 (Proximity Label-MS), FOXP2 (Proximity Label-MS), TNRC18 (Proximity Label-MS), ZEB2 (Proximity Label-MS), EYA4 (Proximity Label-MS), SKI (Proximity Label-MS)

ESM2 similar proteins: A1YEY5, A1YFA5, A1YFI3, A1YG57, A2T733, A2T764, A2T7P4, A6NJ46, O42115, O43248, O43711, O55144, O95096, P02830, P09023, P09024, P09629, P09633, P17509, P17919, P18864, P23410, P28362, P29454, P31259, P31311, P31313, P31315, P42586, P43120, P43345, P43697, P48031, P52951, P53544, P53545, P53546, P56915, P97334, Q02591

Diamond homologs: A0A1W2PPF3, A1YEY5, A1YFI3, A1YG57, A2T733, A2T7P4, A6NLW8, A6NNA5, F1NEA7, G5EBU4, G5EDS1, O18381, O35137, O35160, O42250, O43186, O43316, O43812, O54751, O70137, O73917, O75360, O75364, O95076, P09088, P0CJ85, P0CJ86, P0CJ87, P0CJ88, P0CJ89, P0CJ90, P21711, P22810, P26367, P26630, P29454, P32242, P32243, P34764, P34765

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
EVX1	“down-regulates quantity by repression”	GSC	“transcriptional regulation”
GSC	“down-regulates quantity by repression”	EVX1	“transcriptional regulation”
WWP2	“up-regulates activity”	GSC	ubiquitination
GSC	“down-regulates quantity by repression”	EPHA7	“transcriptional regulation”
GTF2I	“up-regulates quantity by expression”	GSC	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	0
Uncertain significance	58
Likely benign	45
Benign	13

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
126522	NM_173849.3(GSC):c.196_212del (p.Gly66fs)	Pathogenic
126523	NM_173849.3(GSC):c.400C>T (p.Gln134Ter)	Pathogenic
126524	NM_173849.3(GSC):c.355+1G>C	Pathogenic

SpliceAI

238 predictions. Top by Δscore:

Variant	Effect	Δscore
14:94768645:CAGAC:C	acceptor_gain	1.0000
14:94768646:AGAC:A	acceptor_gain	1.0000
14:94768647:GAC:G	acceptor_gain	1.0000
14:94768647:GACC:G	acceptor_loss	1.0000
14:94768648:ACCT:A	acceptor_loss	1.0000
14:94768649:CC:C	acceptor_loss	1.0000
14:94768649:CCTGT:C	acceptor_gain	1.0000
14:94768650:C:CC	acceptor_gain	1.0000
14:94768651:T:C	acceptor_loss	1.0000
14:94768653:T:TC	acceptor_gain	1.0000
14:94768656:C:CT	acceptor_gain	1.0000
14:94768952:GCCTA:G	donor_loss	1.0000
14:94768954:CTACC:C	donor_loss	1.0000
14:94768955:TA:T	donor_loss	1.0000
14:94768956:A:AC	donor_gain	1.0000
14:94768956:ACC:A	donor_loss	1.0000
14:94768956:ACCT:A	donor_gain	1.0000
14:94768957:C:CA	donor_loss	1.0000
14:94768957:C:CC	donor_gain	1.0000
14:94768957:CCT:C	donor_gain	1.0000
14:94768957:CCTC:C	donor_gain	1.0000
14:94768959:T:TA	donor_gain	1.0000
14:94768987:T:A	donor_gain	1.0000
14:94769214:TAGC:T	acceptor_gain	1.0000
14:94769216:GCCTG:G	acceptor_loss	1.0000
14:94769217:CCT:C	acceptor_loss	1.0000
14:94769218:C:CC	acceptor_gain	1.0000
14:94769218:CT:C	acceptor_loss	1.0000
14:94769219:T:G	acceptor_loss	1.0000
14:94768648:AC:A	acceptor_gain	0.9900

AlphaMissense

1645 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:94768612:T:G	Q218P	1.000
14:94768615:C:G	R217P	1.000
14:94768617:C:A	R216S	1.000
14:94768617:C:G	R216S	1.000
14:94768618:C:A	R216M	1.000
14:94768618:C:G	R216T	1.000
14:94768619:T:C	R216G	1.000
14:94768620:C:A	W215C	1.000
14:94768620:C:G	W215C	1.000
14:94768622:A:G	W215R	1.000
14:94768622:A:T	W215R	1.000
14:94768623:T:A	K214N	1.000
14:94768623:T:G	K214N	1.000
14:94768624:T:A	K214I	1.000
14:94768625:T:C	K214E	1.000
14:94768625:T:G	K214Q	1.000
14:94768627:G:A	A213V	1.000
14:94768627:G:T	A213D	1.000
14:94768628:C:G	A213P	1.000
14:94768630:C:G	R212P	1.000
14:94768630:C:T	R212H	1.000
14:94768631:G:A	R212C	1.000
14:94768631:G:C	R212G	1.000
14:94768631:G:T	R212S	1.000
14:94768633:C:A	R211L	1.000
14:94768633:C:G	R211P	1.000
14:94768634:G:A	R211C	1.000
14:94768634:G:C	R211G	1.000
14:94768634:G:T	R211S	1.000
14:94768635:G:C	N210K	1.000

dbSNP variants (sampled 300 via entrez): RS1000043986 (14:94770368 TG>T), RS1000931931 (14:94769613 G>C,T), RS1000982871 (14:94767917 C>T), RS1001132764 (14:94771955 T>C), RS1002830633 (14:94771011 G>T), RS1003139708 (14:94769707 C>A,T), RS1004119935 (14:94771080 C>A,T), RS1004491492 (14:94770767 G>A), RS1005193498 (14:94770126 C>G,T), RS1005496480 (14:94771295 C>G), RS1005853710 (14:94770973 A>G,T), RS1006129717 (14:94768718 G>A), RS1006202219 (14:94769939 G>A,C), RS1007156537 (14:94771346 A>G), RS1007960283 (14:94771374 C>T)

Disease associations

OMIM: gene MIM:138890 | disease phenotypes: MIM:602471

GenCC curated gene-disease

Disease	Classification	Inheritance
short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome	Strong	Autosomal recessive

Mondo (1): short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome (MONDO:0011227)

Orphanet (1): Short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome (Orphanet:397623)

HPO phenotypes

32 total (30 of 32 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000160	Narrow mouth
HP:0000218	High palate
HP:0000252	Microcephaly
HP:0000272	Malar flattening
HP:0000347	Micrognathia
HP:0000405	Conductive hearing impairment
HP:0000413	Atresia of the external auditory canal
HP:0000490	Deeply set eye
HP:0000494	Downslanted palpebral fissures
HP:0000601	Hypotelorism
HP:0000882	Hypoplastic scapulae
HP:0001249	Intellectual disability
HP:0001762	Talipes equinovarus
HP:0002643	Neonatal respiratory distress
HP:0002827	Hip dislocation
HP:0002938	Lumbar hyperlordosis
HP:0003015	Flared metaphysis
HP:0003022	Hypoplasia of the ulna
HP:0003083	Dislocated radial head
HP:0003375	Narrow greater sciatic notch
HP:0003577	Congenital onset
HP:0004322	Short stature
HP:0004467	Preauricular pit
HP:0005792	Short humerus
HP:0006595	Scapulohumeral synostosis
HP:0008785	Delayed ossification of pubic rami
HP:0008905	Rhizomelia
HP:0011968	Feeding difficulties

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST003989_39	Chin dimples	1.000000e-09
GCST003999_10	Nose size	4.000000e-09
GCST004166_50	Nonsyndromic cleft lip with cleft palate	4.000000e-10
GCST006661_88	Male-pattern baldness	3.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0003959	cleft lip

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566544	Short Stature, Auditory Canal Atresia, Mandibular Hypoplasia, Skeletal Abnormalities (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation, increases methylation	3
Tretinoin	affects expression, decreases expression	2
Valproic Acid	affects expression, increases expression	2
IMOL S-140	increases expression	1
terbufos	increases methylation	1
arsenite	increases methylation	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
4-aminophenylarsenoxide	affects binding, decreases reaction	1
pentanal	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	affects binding, decreases reaction	1
Ethanol	increases expression, decreases reaction	1
Arsenic	increases methylation	1
Fonofos	increases methylation	1
Folic Acid	increases expression, decreases reaction	1
Methapyrilene	increases methylation	1
Mianserin	decreases expression	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A2I1	SEES3-1V human GSC, clone1	Embryonic stem cell	Male
CVCL_A2I2	SEES3-1V human GSC, clone2	Embryonic stem cell	Male
CVCL_A2I3	SEES3-1V human GSC, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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