Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	6949
Gene name Gene Name - the full gene name approved by the HGNC.	Treacle ribosome biogenesis factor 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TCOF1
Synonyms (NCBI Gene) Gene synonyms aliases	MFD1, TCS, TCS1, treacle
Chromosome Chromosome number	5
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	5q32-q33.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a nucleolar protein with a LIS1 homology domain. The protein is involved in ribosomal DNA gene transcription through its interaction with upstream binding factor (UBF). Mutations in this gene have been associated with Treacher Collins sy

Show/Hide all(54)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28941769	A>G	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs119470016	C>T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs119470017	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, genic downstream transcript variant
rs148367422	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, genic downstream transcript variant
rs150637771	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, non coding transcript variant
rs377241141	G>T	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, stop gained
rs528897827	GATCTGAAAGTGAGGAGG>-	Likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant, non coding transcript variant, coding sequence variant, inframe deletion
rs587776580	->A	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs587776581	ATAC>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs587776582	AAGAA>-	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs587776583	AGAG>-,AG	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs587776584	AAGGTGAGTGGGACTGCC>-	Pathogenic	Non coding transcript variant, coding sequence variant, splice donor variant, intron variant
rs587776585	AAAAA>-,AAA,AAAA,AAAAAA	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs587777314	->G	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, genic downstream transcript variant
rs748805008	C>A,G,T	Pathogenic, likely-pathogenic	Intron variant, stop gained, missense variant, non coding transcript variant, synonymous variant, coding sequence variant
rs764314276	G>A	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs769931291	C>G,T	Pathogenic	Coding sequence variant, stop gained, missense variant, non coding transcript variant
rs786205575	C>T	Likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, stop gained
rs797046037	CA>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs886041506	G>A	Pathogenic	Splice donor variant
rs886041672	TG>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs896979080	C>G,T	Pathogenic	Non coding transcript variant, missense variant, stop gained, coding sequence variant
rs1057517834	GCAG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1064794474	ACAG>-	Likely-pathogenic, pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1064796606	TG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1064796835	AGAC>GCTGCCTTGGCT	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1266047546	->A	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant
rs1554077988	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, genic downstream transcript variant
rs1554078461	->G	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs1554080460	->G	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs1554080589	GT>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs1554081108	AA>-	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs1554081112	GAAA>-	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs1554081168	CT>-	Pathogenic	Coding sequence variant, stop gained, genic downstream transcript variant
rs1554133681	TG>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554136123	->C	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554137113	->CA	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554137419	AA>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1554137531	CT>-	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1554138811	C>G	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1554138819	AG>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1561540623	->G	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs1562347303	AG>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1581064385	G>A	Likely-pathogenic	Splice donor variant
rs1581075356	CG>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1581114957	->C	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1581136492	G>-	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1581138487	AGTGAGAAAC>-	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs1581203344	C>T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs1581210464	A>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs1581223107	AA>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs1581224630	C>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs1581224984	->C	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs1581226008	AGCAA>-	Likely-pathogenic	Downstream transcript variant, coding sequence variant, genic downstream transcript variant, frameshift variant, non coding transcript variant

Show/Hide all(99)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022519	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT025404	hsa-miR-34a-5p	Proteomics	21566225
MIRT025762	hsa-miR-7-5p	Microarray	19073608
MIRT032257	hsa-let-7b-5p	Proteomics	18668040
MIRT049104	hsa-miR-92a-3p	CLASH	23622248
MIRT048102	hsa-miR-197-3p	CLASH	23622248
MIRT046740	hsa-miR-222-3p	CLASH	23622248
MIRT043611	hsa-miR-151a-3p	CLASH	23622248
MIRT043143	hsa-miR-324-5p	CLASH	23622248
MIRT040570	hsa-miR-92b-3p	CLASH	23622248
MIRT040239	hsa-miR-615-3p	CLASH	23622248
MIRT038780	hsa-miR-93-3p	CLASH	23622248
MIRT037490	hsa-miR-744-5p	CLASH	23622248
MIRT458581	hsa-miR-6847-5p	PAR-CLIP	23592263
MIRT458580	hsa-miR-4257	PAR-CLIP	23592263
MIRT458579	hsa-miR-6786-5p	PAR-CLIP	23592263
MIRT458578	hsa-miR-4252	PAR-CLIP	23592263
MIRT458577	hsa-miR-3689d	PAR-CLIP	23592263
MIRT458576	hsa-miR-6851-5p	PAR-CLIP	23592263
MIRT458575	hsa-miR-3622b-5p	PAR-CLIP	23592263
MIRT458574	hsa-miR-4450	PAR-CLIP	23592263
MIRT458573	hsa-miR-6801-5p	PAR-CLIP	23592263
MIRT458572	hsa-miR-6880-5p	PAR-CLIP	23592263
MIRT458571	hsa-miR-7847-3p	PAR-CLIP	23592263
MIRT458570	hsa-miR-4701-5p	PAR-CLIP	23592263
MIRT458569	hsa-miR-588	PAR-CLIP	23592263
MIRT458568	hsa-miR-6857-5p	PAR-CLIP	23592263
MIRT439477	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT439477	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT458581	hsa-miR-6847-5p	PAR-CLIP	23592263
MIRT458580	hsa-miR-4257	PAR-CLIP	23592263
MIRT458579	hsa-miR-6786-5p	PAR-CLIP	23592263
MIRT458578	hsa-miR-4252	PAR-CLIP	23592263
MIRT458577	hsa-miR-3689d	PAR-CLIP	23592263
MIRT458576	hsa-miR-6851-5p	PAR-CLIP	23592263
MIRT458575	hsa-miR-3622b-5p	PAR-CLIP	23592263
MIRT458574	hsa-miR-4450	PAR-CLIP	23592263
MIRT458573	hsa-miR-6801-5p	PAR-CLIP	23592263
MIRT458572	hsa-miR-6880-5p	PAR-CLIP	23592263
MIRT458571	hsa-miR-7847-3p	PAR-CLIP	23592263
MIRT458570	hsa-miR-4701-5p	PAR-CLIP	23592263
MIRT458569	hsa-miR-588	PAR-CLIP	23592263
MIRT458568	hsa-miR-6857-5p	PAR-CLIP	23592263
MIRT1416629	hsa-miR-1273d	CLIP-seq
MIRT1416630	hsa-miR-1287	CLIP-seq
MIRT1416631	hsa-miR-132	CLIP-seq
MIRT1416632	hsa-miR-194	CLIP-seq
MIRT1416633	hsa-miR-212	CLIP-seq
MIRT1416634	hsa-miR-2467-3p	CLIP-seq
MIRT1416635	hsa-miR-3064-5p	CLIP-seq
MIRT1416636	hsa-miR-3182	CLIP-seq
MIRT1416637	hsa-miR-4659a-3p	CLIP-seq
MIRT1416638	hsa-miR-4659b-3p	CLIP-seq
MIRT1416639	hsa-miR-4687-3p	CLIP-seq
MIRT1416640	hsa-miR-4747-5p	CLIP-seq
MIRT1416641	hsa-miR-4761-5p	CLIP-seq
MIRT1416642	hsa-miR-4778-3p	CLIP-seq
MIRT1416643	hsa-miR-541	CLIP-seq
MIRT1416644	hsa-miR-548ag	CLIP-seq
MIRT1416645	hsa-miR-548ai	CLIP-seq
MIRT1416646	hsa-miR-626	CLIP-seq
MIRT1416647	hsa-miR-654-5p	CLIP-seq
MIRT1416648	hsa-miR-127-5p	CLIP-seq
MIRT1416631	hsa-miR-132	CLIP-seq
MIRT1416632	hsa-miR-194	CLIP-seq
MIRT1416633	hsa-miR-212	CLIP-seq
MIRT1416635	hsa-miR-3064-5p	CLIP-seq
MIRT1416636	hsa-miR-3182	CLIP-seq
MIRT1416649	hsa-miR-3190	CLIP-seq
MIRT1416650	hsa-miR-3202	CLIP-seq
MIRT1416651	hsa-miR-320e	CLIP-seq
MIRT1416652	hsa-miR-4428	CLIP-seq
MIRT1416653	hsa-miR-4533	CLIP-seq
MIRT1416637	hsa-miR-4659a-3p	CLIP-seq
MIRT1416638	hsa-miR-4659b-3p	CLIP-seq
MIRT1416639	hsa-miR-4687-3p	CLIP-seq
MIRT1416640	hsa-miR-4747-5p	CLIP-seq
MIRT1416642	hsa-miR-4778-3p	CLIP-seq
MIRT1416644	hsa-miR-548ag	CLIP-seq
MIRT1416645	hsa-miR-548ai	CLIP-seq
MIRT1416646	hsa-miR-626	CLIP-seq
MIRT2347421	hsa-miR-1183	CLIP-seq
MIRT2347422	hsa-miR-4300	CLIP-seq
MIRT2347423	hsa-miR-4643	CLIP-seq
MIRT2347424	hsa-miR-466	CLIP-seq
MIRT2347425	hsa-miR-4789-3p	CLIP-seq
MIRT2347426	hsa-miR-920	CLIP-seq
MIRT2395602	hsa-miR-3150b-3p	CLIP-seq
MIRT2395603	hsa-miR-4508	CLIP-seq
MIRT2395604	hsa-miR-4693-3p	CLIP-seq
MIRT2395605	hsa-miR-4768-3p	CLIP-seq
MIRT2395606	hsa-miR-4784	CLIP-seq
MIRT2395607	hsa-miR-486-3p	CLIP-seq
MIRT2395608	hsa-miR-665	CLIP-seq
MIRT2461263	hsa-miR-3662	CLIP-seq
MIRT2461264	hsa-miR-4270	CLIP-seq
MIRT2461265	hsa-miR-4441	CLIP-seq
MIRT2461266	hsa-miR-4653-3p	CLIP-seq
MIRT2461267	hsa-miR-580	CLIP-seq

Show/Hide all(19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	TAS	9096354
GO:0001650	Component	Fibrillar center	IDA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0005515	Function	Protein binding	IPI	17620599, 23602568, 25064736, 26399832, 32707033, 32814053, 36411431
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IBA
GO:0005730	Component	Nucleolus	IDA	15249688, 23203802
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	TAS	9096354
GO:0005829	Component	Cytosol	IDA
GO:0006417	Process	Regulation of translation	IMP	26399832
GO:0014029	Process	Neural crest formation	IMP	26399832
GO:0014032	Process	Neural crest cell development	IMP	26399832
GO:0030674	Function	Protein-macromolecule adaptor activity	IDA	26399832
GO:0042790	Process	Nucleolar large rRNA transcription by RNA polymerase I	IBA
GO:0046982	Function	Protein heterodimerization activity	IPI	26399832
GO:0097110	Function	Scaffold protein binding	IBA
GO:0097110	Function	Scaffold protein binding	IPI	23203802

MIM	HGNC	e!Ensembl
606847	11654	ENSG00000070814

Protein

UniProt ID

Q13428

Protein name

Treacle protein (Treacher Collins syndrome protein)

Protein function

Nucleolar protein that acts as a regulator of RNA polymerase I by connecting RNA polymerase I with enzymes responsible for ribosomal processing and modification (PubMed:12777385, PubMed:26399832). Required for neural crest specification: followi

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03546	Treacle	248 → 330	Treacher Collins syndrome protein Treacle	Family
PF03546	Treacle	316 → 427	Treacher Collins syndrome protein Treacle	Family
PF03546	Treacle	422 → 899	Treacher Collins syndrome protein Treacle	Family
PF03546	Treacle	864 → 958	Treacher Collins syndrome protein Treacle	Family

Sequence

MAEARKRRELLPLIYHHLLRAGYVRAAREVKEQSGQKCFLAQPVTLLDIYTHWQQTSELG
RKRKAEEDAALQAKKTRVSDPISTSESSEEEEEAEAETAKATPRLASTNSSVLGADLPSS
MKEKAKAETEKAGKTGNSMPHPATGKTVANLLSGKSPRKSAEPSANTTLVSETEEEGSVP
AFGAAAKPGMVSAGQADSSSEDTSSSSDETDVEGKPSVKPAQVKASSVSTKESPARKAAP
APGKVGDVTPQVKGGALPPAKRAKKPEEESESSEEGSESEEEAPAGTRSQVKASEKILQV
RAASAPAKGTPGKGATPAPPGKAGAVASQTKAGKPEEDSESSSEESSDSEEETPAAKALL
QAKASGKTSQVGAASAPAKESPRKGAAPAPPGKTGPAVAKAQAGKREEDSQSSSEESDSE
EEAPAQAKPSGKAPQVRAASAPAKESPRKGAAPAPPRKTGPAAAQVQVGKQEEDSRSSSE
ESDSDREALAAMNAAQVKPLGKSPQVKPASTMGMGPLGKGAGPVPPGKVGPATPSAQVGK
WEEDSESSSEESSDSSDGEVPTAVAPAQEKSLGNILQAKPTSSPAKGPPQKAGPVAVQVK
AEKPMDNSESSEESSDSADSEEAPAAMTAAQAKPALKIPQTKACPKKTNTTASAKVAPVR
VGTQAPRKAGTATSPAGSSPAVAGGTQRPAEDSSSSEESDSEEEKTGLAVTVGQAKSVGK
GLQVKAASVPVKGSLGQGTAPVLPGKTGPTVTQVKAEKQEDSESSEEESDSEEAAASPAQ
VKTSVKKTQAKANPAAARAPSAKGTISAPGKVVTAAAQAKQRSPSKVKPPVRNPQNSTVL
ARGPASVPSVGKAVATAAQAQTGPEEDSGSSEEESDSEEEAETLAQVKPSGKTHQIRAAL
APAKESPRKGAAPTPPGKTGPSAAQAGKQDDSGSSSEESDSDGEAPAAVTSAQVIKPPLI
FVDPNRSPAGPAATPAQAQAASTPRKARASESTARSSSSESEDEDVIPATQCLTPGIRTN
VVTMPTAHPRIAPKASMAGASSSKESSRISDGKKQEGPATQVSKKNPASLPLTQAALKVL
AQKASEAQPPVARTQPSSGVDSAVGTLPATSPQSTSVQAKGTNKLRKPKLPEVQQATKAP
ESSDDSEDSSDSSSGSEEDGEGPQGAKSAHTLGPTPSRTETLVEETAAESSEDDVVAPSQ
SLLSGYMTPGLTPANSQASKATPKLDSSPSVSSTLAAKDDPDGKQEAKPQQAAGMLSPKT
GGKEAASGTTPQKSRKPKKGAGNPQASTLALQSNITQCLLGQPWPLNEAQVQASVVKVLT
ELLEQERKKVVDTTKESSRKGWESRKRKLSGDQPAARTPRSKKKKKLGAGEGGEASVSPE
KTSTTSKGKAKRDKASGDVKEKKGKGSLGSQGAKDEPEEELQKGMGTVEGGDQSNPKSKK
EKKKSDKRKKDKEKKEKKKKAKKASTKDSESPSQKKKKKKKKTAEQTV

Sequence length

1488

Interactions

View interactions

	KEGG
	Ribosome biogenesis in eukaryotes

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Treacher Collins syndrome	Treacher Collins syndrome 1	rs1581224630, rs587776583, rs764314276, rs1554078461, rs1767064064, rs119470017, rs748805008, rs1562347303, rs35868965, rs587776584, rs1554080589, rs1561540623, rs1767850450, rs587776585, rs1554081112 View all (26 more)	N/A
treacher collins syndrome	Treacher Collins syndrome	rs587776582	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Microcephaly	microcephaly	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (30)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acrofacial dysostosis Nager type	Associate	32537850
Adenocarcinoma	Associate	27600491
Auriculoosteodysplasia	Associate	21150135
Birt Hogg Dube Syndrome	Associate	27871249
Bovine Respiratory Disease Complex	Associate	9074926
Carcinogenesis	Associate	35093935
Carcinoma Hepatocellular	Associate	36524514
Cell Transformation Neoplastic	Associate	27600491
Chromosome Deletion	Inhibit	23695276
Cleft Palate	Associate	18688869, 8037214
Craniofacial Abnormalities	Associate	12777385, 40390636
Deafness	Associate	36656851
Deafness Progressive With Stapes Fixation	Associate	32351010
Dental Caries	Associate	33277566
Developmental Disabilities	Associate	39518953
GSD IV Neuromuscular Form Fatal Perinatal	Associate	36656851
Hearing Loss	Associate	36656851
Hearing Loss Conductive	Associate	8037214
Heart Diseases	Associate	25790162
Intellectual Disability	Associate	23695276, 39518953
Kininogen Deficiency High Molecular Weight and Low Molecular Weight	Associate	25790162
Mandibulofacial Dysostosis	Associate	10982400, 12777385, 16801042, 17431905, 19107148, 20003452, 20340163, 21951868, 22317976, 22415350, 23695276, 24603435, 25064736, 25512513, 25790162 View all (20 more)
Neoplasms	Associate	35093935
Noonan Syndrome	Associate	28921562
Orofacial Cleft 1	Associate	18688869
Orofaciodigital syndrome 11	Associate	32543076
Perivascular Epithelioid Cell Neoplasms	Associate	33180365
Triple Negative Breast Neoplasms	Associate	39523372
Virus Diseases	Associate	36135364
X Linked Combined Immunodeficiency Diseases	Associate	27600491

TCOF1 (treacle ribosome biogenesis factor 1)