CCDC47

Summary

CCDC47 (coiled-coil domain containing 47, HGNC:24856) is a protein-coding gene on chromosome 17q23.3, encoding PAT complex subunit CCDC47 (Q96A33). Component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes.

Enables protein folding chaperone and ribosome binding activity. Involved in ERAD pathway; endoplasmic reticulum calcium ion homeostasis; and multi-pass transmembrane protein insertion into ER membrane. Located in endoplasmic reticulum membrane. Part of multi-pass translocon complex and protein folding chaperone complex.

Source: NCBI Gene 57003 — RefSeq curated summary.

At a glance

• Gene–disease (curated): trichohepatoneurodevelopmental syndrome (Definitive, GenCC)
• Clinical variants (ClinVar): 87 total — 1 pathogenic, 5 likely-pathogenic
• Phenotypes (HPO): 82
• Druggable target: yes
• MANE Select transcript: NM_020198

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24856
Approved symbol	CCDC47
Name	coiled-coil domain containing 47
Location	17q23.3
Locus type	gene with protein product
Status	Approved
Aliases	GK001
Ensembl gene	ENSG00000108588
Ensembl biotype	protein_coding
OMIM	618260
Entrez	57003

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 29 protein_coding, 2 retained_intron

ENST00000225726, ENST00000403162, ENST00000580986, ENST00000582252, ENST00000582331, ENST00000584112, ENST00000878791, ENST00000878792, ENST00000878793, ENST00000878794, ENST00000878795, ENST00000878796, ENST00000878797, ENST00000878798, ENST00000878799, ENST00000878800, ENST00000878801, ENST00000916946, ENST00000916947, ENST00000916948, ENST00000916949, ENST00000960669, ENST00000960670, ENST00000960671, ENST00000960672, ENST00000960673, ENST00000960674, ENST00000960675, ENST00000960676, ENST00000960677, ENST00000960678

RefSeq mRNA: 1 — MANE Select: NM_020198 NM_020198

CCDS: CCDS11643

Canonical transcript exons

ENST00000225726 — 13 exons

Exon	Start	End
ENSE00000555654	63761230	63761351
ENSE00000742037	63751940	63752107
ENSE00000742039	63752741	63752799
ENSE00000742049	63764016	63764190
ENSE00000742051	63764740	63764847
ENSE00000742053	63765912	63766194
ENSE00000857864	63752320	63752429
ENSE00000857866	63754433	63754518
ENSE00001347617	63745255	63746961
ENSE00001553059	63773412	63773597
ENSE00003468323	63756469	63756570
ENSE00003560640	63760914	63760979
ENSE00003664439	63756240	63756350

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 81.2546 / max 1010.8774, expressed in 1826 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
167484	80.9105	1826
167485	0.3441	172

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.03	gold quality
islet of Langerhans	UBERON:0000006	97.79	gold quality
rectum	UBERON:0001052	97.30	gold quality
tendon	UBERON:0000043	97.29	gold quality
heart right ventricle	UBERON:0002080	97.19	gold quality
parotid gland	UBERON:0001831	96.99	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.99	gold quality
colonic mucosa	UBERON:0000317	96.72	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.57	gold quality
biceps brachii	UBERON:0001507	96.48	gold quality
gastrocnemius	UBERON:0001388	96.47	gold quality
muscle of leg	UBERON:0001383	96.33	gold quality
cervix squamous epithelium	UBERON:0006922	96.10	gold quality
cartilage tissue	UBERON:0002418	96.04	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	95.99	gold quality
palpebral conjunctiva	UBERON:0001812	95.89	gold quality
tendon of biceps brachii	UBERON:0008188	95.89	gold quality
colonic epithelium	UBERON:0000397	95.79	gold quality
left adrenal gland	UBERON:0001234	95.60	gold quality
pancreas	UBERON:0001264	95.54	gold quality
adrenal gland	UBERON:0002369	95.43	gold quality
gall bladder	UBERON:0002110	95.41	gold quality
right adrenal gland	UBERON:0001233	95.40	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.40	gold quality
adrenal tissue	UBERON:0018303	95.33	gold quality
left adrenal gland cortex	UBERON:0035825	95.28	gold quality
right adrenal gland cortex	UBERON:0035827	95.24	gold quality
right atrium auricular region	UBERON:0006631	95.13	gold quality
duodenum	UBERON:0002114	95.12	gold quality
stromal cell of endometrium	CL:0002255	95.11	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-HCAD-13	no	3.17
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

147 targeting CCDC47, 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-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502

Literature-anchored findings (GeneRIF, showing 1)

• these findings suggested that calumin serves to maintain the yolk sac integrity through participation in the ERAD activity, contributing to embryonic development. (PMID:25009997)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc47	ENSDARG00000054362
mus_musculus	Ccdc47	ENSMUSG00000078622
rattus_norvegicus	Ccdc47	ENSRNOG00000009006
drosophila_melanogaster	CG17593	FBGN0031544
caenorhabditis_elegans		WBGENE00014204

Protein

Protein identifiers

PAT complex subunit CCDC47 — Q96A33 (reviewed: Q96A33)

Alternative names: Calumin, Coiled-coil domain-containing protein 47

All UniProt accessions (2): Q96A33, J3KRX4

UniProt curated annotations — full annotation on UniProt →

Function. Component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. The MPT complex takes over after the SEC61 complex: following membrane insertion of the first few transmembrane segments of proteins by the SEC61 complex, the MPT complex occludes the lateral gate of the SEC61 complex to promote insertion of subsequent transmembrane regions. Within the MPT complex, the PAT subcomplex sequesters any highly polar regions in the transmembrane domains away from the non-polar membrane environment until they can be buried in the interior of the fully assembled protein. Within the PAT subcomplex, CCDC47 occludes the lateral gate of the SEC61 complex. Involved in the regulation of calcium ion homeostasis in the ER. Required for proper protein degradation via the ERAD (ER-associated degradation) pathway. Has an essential role in the maintenance of ER organization during embryogenesis.

Subunit / interactions. Component of the PAT complex, composed of WDR83OS/Asterix and CCDC47. The PAT complex is part of the multi-pass translocon (MPT) complex, composed of three subcomplexes, the GEL complex (composed of RAB5IF/OPTI and TMCO1), the BOS complex (composed of NCLN/Nicalin, NOMO and TMEM147) and the PAT complex (composed of WDR83OS/Asterix and CCDC47). The MPT complex associates with the SEC61 complex. Interacts with VCP, HSPA5, DERL1, DERL2 and SELENOS.

Subcellular location. Endoplasmic reticulum membrane. Rough endoplasmic reticulum membrane.

Disease relevance. Trichohepatoneurodevelopmental syndrome (THNS) [MIM:618268] An autosomal recessive complex multisystem disorder characterized by woolly or coarse hair, liver dysfunction, pruritus, dysmorphic features, hypotonia, and global developmental delay. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the CCDC47 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96A33-1	1	yes
Q96A33-2	2

RefSeq proteins (1): NP_064583* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012879	CCDC47	Family

Pfam: PF07946

UniProt features (17 total): compositionally biased region 4, sequence variant 2, topological domain 2, region of interest 2, signal peptide 1, chain 1, glycosylation site 1, splice variant 1, sequence conflict 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6W6L	ELECTRON MICROSCOPY	3.84

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96A33-F1	77.07	0.46

Functional residue map

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

Glycosylation sites (1): 178

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 424 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, ACTACCT_MIR196A_MIR196B, GOBP_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_OSTEOBLAST_DIFFERENTIATION, GOBP_PROTEIN_MATURATION, GOBP_ER_NUCLEUS_SIGNALING_PATHWAY, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_PROTEIN_FOLDING, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_ENDOPLASMIC_RETICULUM_CALCIUM_ION_HOMEOSTASIS, GOBP_OSSIFICATION, TCCAGAT_MIR5165P, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE

GO Biological Process (10): osteoblast differentiation (GO:0001649), ER overload response (GO:0006983), post-embryonic development (GO:0009791), endoplasmic reticulum calcium ion homeostasis (GO:0032469), ERAD pathway (GO:0036503), protein insertion into ER membrane (GO:0045048), multi-pass transmembrane protein insertion into ER membrane (GO:0160063), protein folding (GO:0006457), endoplasmic reticulum organization (GO:0007029), calcium ion homeostasis (GO:0055074)

GO Molecular Function (5): RNA binding (GO:0003723), calcium ion binding (GO:0005509), ribosome binding (GO:0043022), protein folding chaperone (GO:0044183), protein binding (GO:0005515)

GO Cellular Component (7): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), rough endoplasmic reticulum membrane (GO:0030867), protein folding chaperone complex (GO:0101031), multi-pass translocon complex (GO:0160064), rough endoplasmic reticulum (GO:0005791)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to endoplasmic reticulum stress	2
endoplasmic reticulum	2
ossification	1
cell differentiation	1
ER-nucleus signaling pathway	1
cellular response to biotic stimulus	1
multicellular organism development	1
multicellular organismal process	1
intracellular calcium ion homeostasis	1
proteasomal protein catabolic process	1
response to chemical	1
endoplasmic reticulum organization	1
protein localization to organelle	1
protein insertion into membrane	1
protein insertion into ER membrane	1
cellular process	1
protein maturation	1
organelle organization	1
endomembrane system organization	1
monoatomic cation homeostasis	1
inorganic ion homeostasis	1
nucleic acid binding	1
metal ion binding	1
ribonucleoprotein complex binding	1
molecular_function	1
protein folding	1
binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1
endoplasmic reticulum membrane	1
rough endoplasmic reticulum	1
bounding membrane of organelle	1
intracellular protein-containing complex	1
ER membrane insertion complex	1

Protein interactions and networks

STRING

1462 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC47	TMCO1	Q9UM00	787
CCDC47	SEC61A1	P38378	655
CCDC47	ANKZF1	Q9H8Y5	568
CCDC47	ERLIN1	O75477	564
CCDC47	TMEM147	Q9BVK8	534
CCDC47	NCLN	Q969V3	507
CCDC47	WDR83OS	Q9Y284	486
CCDC47	TCP11L1	Q9NUJ3	472
CCDC47	EMC3	Q9P0I2	465
CCDC47	TRAM1	Q15629	448
CCDC47	SEC61A2	Q9H9S3	422
CCDC47	STT3A	P46977	420
CCDC47	TRAM1L1	Q8N609	407
CCDC47	TMEM208	Q9BTX3	404
CCDC47	BPNT2	Q9NX62	400

IntAct

195 interactions, top by confidence:

A	B	Type	Score
TIRAP	TLR4	psi-mi:“MI:0914”(association)	0.810
EMC7	EMC8	psi-mi:“MI:0914”(association)	0.790
EMC3	EMC8	psi-mi:“MI:0914”(association)	0.730
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
IGF1R	PIK3R2	psi-mi:“MI:2364”(proximity)	0.590
INSR	PIK3R2	psi-mi:“MI:2364”(proximity)	0.570
PRKCA	CCDC47	psi-mi:“MI:0915”(physical association)	0.560
CCDC47	YWHAG	psi-mi:“MI:0915”(physical association)	0.560
CCDC47	SETDB1	psi-mi:“MI:0915”(physical association)	0.560
CCDC47	KAT5	psi-mi:“MI:0915”(physical association)	0.560
LMO3	CCDC47	psi-mi:“MI:0915”(physical association)	0.560
CCDC47	WDR83OS	psi-mi:“MI:0915”(physical association)	0.560
ILK	HAX1	psi-mi:“MI:0914”(association)	0.530
RPN1	APBB1	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
APLNR	SLC33A1	psi-mi:“MI:0914”(association)	0.530

BioGRID (626): CCDC47 (Affinity Capture-MS), CCDC47 (Affinity Capture-MS), CCDC47 (Affinity Capture-MS), CCDC47 (Co-fractionation), CCDC47 (Co-fractionation), CCDC47 (Co-fractionation), CCDC47 (Co-fractionation), CCDC47 (Co-fractionation), CCDC47 (Co-fractionation), CCDC47 (Co-fractionation), CCDC47 (Affinity Capture-MS), CCDC47 (Proximity Label-MS), CCDC47 (Proximity Label-MS), CCDC47 (Proximity Label-MS), CCDC47 (Proximity Label-MS)

ESM2 similar proteins: A0A8I3P7X4, A7S641, A8WG88, A9ULY7, B0R034, B0W6N3, B5DFC8, B5ME19, D6WIX5, E7EXT2, F7AEX0, O60308, O95202, P0C204, P45433, P53569, Q03701, Q0VA06, Q173M7, Q1L987, Q28HX4, Q3SYW6, Q3ZC50, Q4QR58, Q5RAT8, Q5RCI4, Q5U2X6, Q5XGZ8, Q5XIN6, Q5ZK33, Q66I12, Q6AZI2, Q6IVW0, Q6P1V4, Q6PFQ2, Q6PGY6, Q7PGE8, Q7SYB2, Q8BZN6, Q8R1B4

Diamond homologs: A0A8I3P7X4, P0C204, Q3ZC50, Q5RCI4, Q5U2X6, Q66I12, Q6AZI2, Q96A33, Q9D024, Q94CC0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CCDC47	“form complex”	“PAT intramembrane chaperone complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 216 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
PD-L1(CD274) glycosylation and translocation to plasma membrane	6	23.1×	3e-05
Regulation of CDH1 posttranslational processing and trafficking to plasma membrane	7	17.4×	3e-05
Maturation of spike protein	8	15.7×	2e-05
FCERI mediated MAPK activation	5	12.8×	1e-03
Maturation of DENV proteins	7	11.0×	3e-04
Regulation of RAS by GAPs	7	10.0×	3e-04
Signaling by SCF-KIT	5	9.2×	5e-03
SPOP-mediated proteasomal degradation of PD-L1(CD274)	5	8.5×	6e-03

GO biological processes:

GO term	Partners	Fold	FDR
tail-anchored membrane protein insertion into ER membrane	7	37.2×	2e-07
obsolete protein N-linked glycosylation via asparagine	5	19.1×	2e-03
protein N-linked glycosylation	6	9.0×	9e-03
ERAD pathway	7	7.2×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	5
Uncertain significance	52
Likely benign	6
Benign	5

Top pathogenic / likely-pathogenic (6)

Variant ID	HGVS	Classification
1697227	NM_020198.3(CCDC47):c.563del (p.Asn188fs)	Pathogenic
1526240	NM_020198.3(CCDC47):c.1211_1232dup (p.Ala411_Arg412insLysSerArgTer)	Likely pathogenic
562185	NM_020198.3(CCDC47):c.1165del (p.Ser389fs)	Likely pathogenic
562186	NM_020198.3(CCDC47):c.811C>T (p.Arg271Ter)	Likely pathogenic
562187	NM_020198.3(CCDC47):c.1145del (p.Leu382fs)	Likely pathogenic
993035	NM_020198.3(CCDC47):c.567_570del (p.Glu190fs)	Likely pathogenic

SpliceAI

2656 predictions. Top by Δscore:

Variant	Effect	Δscore
17:63751935:CTAA:C	donor_loss	1.0000
17:63751938:ACCTC:A	donor_loss	1.0000
17:63751939:C:CA	donor_loss	1.0000
17:63751941:T:TA	donor_gain	1.0000
17:63751968:T:TA	donor_gain	1.0000
17:63752103:TTGCC:T	acceptor_loss	1.0000
17:63752109:T:C	acceptor_loss	1.0000
17:63752114:C:CT	acceptor_gain	1.0000
17:63752114:C:T	acceptor_gain	1.0000
17:63752115:A:T	acceptor_gain	1.0000
17:63752318:A:AC	donor_gain	1.0000
17:63752319:C:CC	donor_gain	1.0000
17:63752319:CTT:C	donor_gain	1.0000
17:63752319:CTTCT:C	donor_gain	1.0000
17:63752321:T:TA	donor_gain	1.0000
17:63752430:C:CC	acceptor_gain	1.0000
17:63752735:ACTT:A	donor_loss	1.0000
17:63752736:CTTA:C	donor_loss	1.0000
17:63752737:TTACC:T	donor_loss	1.0000
17:63752738:TA:T	donor_loss	1.0000
17:63752739:A:AC	donor_gain	1.0000
17:63752739:AC:A	donor_gain	1.0000
17:63752740:C:CG	donor_gain	1.0000
17:63752740:CC:C	donor_gain	1.0000
17:63752740:CCA:C	donor_gain	1.0000
17:63752795:CTTCC:C	acceptor_gain	1.0000
17:63752798:CC:C	acceptor_gain	1.0000
17:63752798:CCCTG:C	acceptor_loss	1.0000
17:63752799:CC:C	acceptor_gain	1.0000
17:63752799:CCTGT:C	acceptor_loss	1.0000

AlphaMissense

3268 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:63751944:A:G	L456P	1.000
17:63751950:C:G	R454P	1.000
17:63751983:C:G	R443P	1.000
17:63751996:C:G	A439P	1.000
17:63751997:T:A	R438S	1.000
17:63751997:T:G	R438S	1.000
17:63752013:C:G	R433P	1.000
17:63752016:C:G	R432P	1.000
17:63752022:T:G	Q430P	1.000
17:63752026:C:G	A429P	1.000
17:63752029:C:G	A428P	1.000
17:63752034:T:G	Q426P	1.000
17:63752036:T:A	R425S	1.000
17:63752036:T:G	R425S	1.000
17:63752037:C:G	R425T	1.000
17:63752047:G:C	H422D	1.000
17:63752082:C:G	R410P	1.000
17:63752083:G:T	R410S	1.000
17:63760968:T:A	R227S	1.000
17:63760968:T:G	R227S	1.000
17:63760969:C:A	R227I	1.000
17:63760969:C:G	R227T	1.000
17:63761264:C:G	R212P	1.000
17:63761272:A:C	C209W	1.000
17:63761274:A:G	C209R	1.000
17:63761277:A:G	W208R	1.000
17:63761277:A:T	W208R	1.000
17:63761279:A:G	L207P	1.000
17:63761351:C:T	G183E	1.000
17:63764016:C:G	G183R	1.000

dbSNP variants (sampled 300 via entrez): RS1000152938 (17:63748883 G>A,C), RS1000180475 (17:63770575 T>A), RS1000222400 (17:63750698 C>G), RS1000245500 (17:63762293 AT>A,ATT), RS1000319456 (17:63761997 A>G), RS1000429387 (17:63763398 G>A), RS1000482102 (17:63755778 A>C), RS1000485798 (17:63769250 A>G), RS1000503967 (17:63749265 G>A), RS1000517911 (17:63768929 T>C,G), RS1000526451 (17:63768587 C>G,T), RS1000851005 (17:63756113 T>C), RS1000862509 (17:63763064 C>A), RS1000878023 (17:63773486 G>C,T), RS1000972387 (17:63773621 C>G,T)

Disease associations

OMIM: gene MIM:618260 | disease phenotypes: MIM:618268

GenCC curated gene-disease

Disease	Classification	Inheritance
trichohepatoneurodevelopmental syndrome	Definitive	Autosomal recessive

Mondo (1): trichohepatoneurodevelopmental syndrome (MONDO:0032645)

Orphanet (0):

HPO phenotypes

82 total (30 of 82 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000154	Wide mouth
HP:0000158	Macroglossia
HP:0000218	High palate
HP:0000248	Brachycephaly
HP:0000252	Microcephaly
HP:0000280	Coarse facial features
HP:0000286	Epicanthus
HP:0000316	Hypertelorism
HP:0000341	Narrow forehead
HP:0000369	Low-set ears
HP:0000403	Recurrent otitis media
HP:0000414	Bulbous nose
HP:0000483	Astigmatism
HP:0000508	Ptosis
HP:0000527	Long eyelashes
HP:0000540	Hypermetropia
HP:0000656	Ectropion
HP:0000664	Synophrys
HP:0000678	Dental crowding
HP:0000687	Widely spaced teeth
HP:0000691	Microdontia
HP:0000767	Pectus excavatum
HP:0000774	Narrow chest
HP:0000821	Hypothyroidism
HP:0000989	Pruritus
HP:0001081	Cholelithiasis
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001265	Hyporeflexia

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067137 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.87	Kd	136.3	nM	CHEMBL3752910
6.87	ED50	136.3	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148009: Binding affinity to human CCDC47 incubated for 45 mins by Kinobead based pull down assay	kd	0.1363	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, affects cotreatment, increases expression	4
bisphenol A	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	increases expression	1
aflatoxin B2	increases methylation	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
bisphenol S	decreases expression, affects cotreatment	1
LDN 193189	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects methylation	1
Clozapine	increases expression, affects cotreatment	1
Coumestrol	increases expression	1
Cuprizone	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Estradiol	affects binding, increases reaction	1
Hydralazine	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Isoniazid	decreases expression	1
Ivermectin	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651051	Binding	Binding affinity to human CCDC47 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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