Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	9533
Gene name	RNA polymerase I and III subunit C
Gene symbol	POLR1C
Synonyms (NCBI Gene)	AC40HLD11RPA39RPA40RPA5RPAC1RPC40TCS3
Chromosome	6
Chromosome location	6p21.1
Summary	The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinat

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SNP ID	Visualize variation	Clinical significance	Consequence
rs141156009	C>T	Pathogenic	Missense variant, coding sequence variant
rs141471029	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs148385032	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs181576159	C>T	Pathogenic	Intron variant, coding sequence variant, missense variant
rs191582628	G>A,C	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs201320592	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs371802902	A>G	Pathogenic	Missense variant, coding sequence variant
rs373046018	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs387907020	A>T	Pathogenic	Stop gained, coding sequence variant, intron variant
rs751006626	T>C	Pathogenic	Coding sequence variant, missense variant
rs763593155	C>A,G,T	Pathogenic	Synonymous variant, coding sequence variant, stop gained
rs767639108	TATAT>-	Pathogenic	Coding sequence variant, frameshift variant
rs770637715	A>T	Pathogenic	Coding sequence variant, missense variant
rs770857344	AA>-	Pathogenic	Coding sequence variant, frameshift variant
rs772343871	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs773388338	G>A	Pathogenic	Coding sequence variant, missense variant
rs780663139	G>-	Likely-pathogenic	Stop gained, coding sequence variant
rs796052125	T>C	Pathogenic	Missense variant, coding sequence variant
rs796052127	G>A,T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs875989826	AAG>-	Likely-pathogenic, pathogenic	Inframe deletion, coding sequence variant
rs1015942660	C>T	Pathogenic	Missense variant, coding sequence variant
rs1057519456	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1156407486	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1255115751	C>T	Pathogenic	Coding sequence variant, missense variant
rs1305006253	T>C	Pathogenic	Coding sequence variant, missense variant
rs1554131502	T>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1582181247	G>C	Pathogenic	Missense variant, coding sequence variant
rs1582184344	G>A	Pathogenic	Missense variant, coding sequence variant, intron variant

miRTarBase ID	miRNA	Experiments	Reference
MIRT032027	hsa-miR-16-5p	Proteomics	18668040
MIRT1248317	hsa-miR-4698	CLIP-seq
MIRT1248318	hsa-miR-495	CLIP-seq
MIRT1248317	hsa-miR-4698	CLIP-seq
MIRT1248318	hsa-miR-495	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000428	Component	DNA-directed RNA polymerase complex	IEA
GO:0001650	Component	Fibrillar center	IDA
GO:0003677	Function	DNA binding	IEA
GO:0003899	Function	DNA-directed RNA polymerase activity	IBA
GO:0003899	Function	DNA-directed RNA polymerase activity	IEA
GO:0003899	Function	DNA-directed RNA polymerase activity	TAS	9540830
GO:0005515	Function	Protein binding	IPI	16189514, 21988832, 25416956, 27107012, 31515488, 32296183, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IDA	33335104
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005666	Component	RNA polymerase III complex	IBA
GO:0005666	Component	RNA polymerase III complex	IDA	24107381, 33335104, 34675218
GO:0005730	Component	Nucleolus	IEA
GO:0005736	Component	RNA polymerase I complex	IBA
GO:0005736	Component	RNA polymerase I complex	IDA	34671025, 36271492
GO:0005736	Component	RNA polymerase I complex	IEA
GO:0005736	Component	RNA polymerase I complex	TAS	9540830
GO:0005737	Component	Cytoplasm	IDA	33335104
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006351	Process	DNA-templated transcription	IEA
GO:0006360	Process	Transcription by RNA polymerase I	TAS	9540830
GO:0046983	Function	Protein dimerization activity	IEA

MIM	HGNC	e!Ensembl
610060	20194	ENSG00000171453

O15160

Protein name

DNA-directed RNA polymerases I and III subunit RPAC1 (DNA-directed RNA polymerase I subunit C) (RNA polymerases I and III subunit AC1) (AC40) (DNA-directed RNA polymerases I and III 40 kDa polypeptide) (RPA40) (RPA39) (RPC40)

Protein function

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and short non-coding RNAs

PDB

7A6H , 7AE1 , 7AE3 , 7AEA , 7AST , 7D58 , 7D59 , 7DN3 , 7DU2 , 7FJI , 7FJJ , 7OB9 , 7OBA , 7OBB , 7VBA , 7VBB , 7VBC , 8A43 , 8ITY , 8IUE , 8IUH , 9FSO , 9FSP , 9FSQ , 9FSR , 9FSS

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01000	RNA_pol_A_bac	92 → 226	RNA polymerase Rpb3/RpoA insert domain	Domain
PF01193	RNA_pol_L	62 → 333	RNA polymerase Rpb3/Rpb11 dimerisation domain	Domain

Sequence

MAASQAVEEMRSRVVLGEFGVRNVHTTDFPGNYSGYDDAWDQDRFEKNFRVDVVHMDENS
LEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRLGLIPIHADPR
LFEYRNQGDEEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHKVYTRHMTWIPLGN
QADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDIT
LLEPVEGEAAEELSRCFSPGVIEVQEVQGKKVARVANPRLDTFSREIFRNEKLKKVVRLA
RVRDHYIFSVESTGVLPPDVLVSEAIKVLMGKCRRFLDELDAVQMD

Sequence length

346

Interactions

View interactions

KEGG Pathway	Reactome Pathway
RNA polymerase	Cytosolic sensors of pathogen-associated DNA
Cytosolic DNA-sensing pathway	B-WICH complex positively regulates rRNA expression
	RNA Polymerase I Transcription Initiation
	RNA Polymerase I Promoter Escape
	RNA Polymerase I Transcription Termination
	RNA Polymerase III Transcription Initiation From Type 1 Promoter
	RNA Polymerase III Transcription Initiation From Type 2 Promoter
	RNA Polymerase III Transcription Initiation From Type 3 Promoter

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hypomyelinating leukodystrophy 11	Likely pathogenic; Pathogenic	rs2127691140, rs1793021342, rs1561856961, rs796052124, rs796052125, rs796052126, rs796052127, rs780663139, rs886041661, rs763593155, rs1793020065, rs1057519455, rs1057519456, rs191582628, rs141156009 View all (12 more)	RCV005038324 RCV002506921 RCV002221865 RCV000186585 RCV000186586 View all (22 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
POLR1C-related disorder	Likely pathogenic; Pathogenic	rs796052127, rs2482891698, rs1057519455, rs191582628	RCV003387792 RCV004542633 RCV006263922 RCV002281718	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Treacher Collins syndrome 3	Likely pathogenic; Pathogenic	rs2127691140, rs1793021342, rs796052127, rs780663139, rs886041661, rs1057519455, rs191582628, rs1335699710, rs387907020, rs2127686639, rs141156009, rs1554131502, rs1156407486, rs767639108	RCV005038324 RCV002506921 RCV000853238 RCV000490296 RCV005031844 View all (9 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal. Show/Hide Unknown Diseases (13)
CEREBELLAR ATAXIA, EARLY ONSET	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Uncertain significance	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hearing impairment	Uncertain significance; Conflicting classifications of pathogenicity	ClinVar Disgenet	—	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
LEUKODYSTROPHY, HYPOMYELINATING, 11	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, WITH HYPODONTIA AND HYPOGONADOTROPIC HYPOGONADISM	—	Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Uncertain significance	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MANDIBULOFACIAL DYSOSTOSIS	—	CTD, Disgenet CTD, Disgenet	21131976	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MANDIBULOFACIAL DYSOSTOSIS, TREACHER COLLINS TYPE, AUTOSOMAL RECESSIVE	—	CTD, Disgenet CTD, Disgenet	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Treacher Collins Syndrome, Recessive	Uncertain significance	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREACHER-COLLINS SYNDROME	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	20301704, 20301704	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
POLR1D	2	["Mandibulofacial dysostosis","Treacher collins syndrome"]	10	["RNA polymerase","Cytosolic DNA-sensing pathway","RNA Polymerase I Transcription Termination","RNA Polymerase I Transcription Initiation","RNA Polymerase I Promoter Escape","B-WICH complex positively regulates rRNA expression","RNA Polymerase III Transcription Initiation From Type 3 Promoter","Cytosolic sensors of pathogen-associated DNA ","RNA Polymerase III Transcription Initiation From Type 1 Promoter","RNA Polymerase III Transcription Initiation From Type 2 Promoter"]	7	["Disgenet (Hearing loss)","Disgenet (Mandibulofacial dysostosis)","CTD (Mandibulofacial dysostosis)","ClinVar (Treacher collins syndrome)","HPO (Treacher collins syndrome)","ClinGen (Treacher collins syndrome)","Orphanet (Treacher collins syndrome)"]
POLR1B	2	["Mandibulofacial dysostosis","Treacher collins syndrome"]	5	["RNA polymerase","RNA Polymerase I Transcription Termination","RNA Polymerase I Transcription Initiation","RNA Polymerase I Promoter Escape","B-WICH complex positively regulates rRNA expression"]	5	["Disgenet (Mandibulofacial dysostosis)","ClinVar (Treacher collins syndrome)","HPO (Treacher collins syndrome)","ClinGen (Treacher collins syndrome)","Orphanet (Treacher collins syndrome)"]
POLR3B	2	["Cerebellar ataxia","Hypomyelinating leukodystrophy"]	6	["RNA polymerase","Cytosolic DNA-sensing pathway","RNA Polymerase III Transcription Initiation From Type 3 Promoter","Cytosolic sensors of pathogen-associated DNA ","RNA Polymerase III Transcription Initiation From Type 1 Promoter","RNA Polymerase III Transcription Initiation From Type 2 Promoter"]	6	["Disgenet (Cerebellar ataxia)","ClinVar (Hypomyelinating leukodystrophy)","GenCC (Hypomyelinating leukodystrophy)","Disgenet (Hypomyelinating leukodystrophy)","CTD (Hypomyelinating leukodystrophy)","HPO (Hypomyelinating leukodystrophy)"]
TCOF1	2	["Mandibulofacial dysostosis","Treacher collins syndrome"]	0	[]	7	["Disgenet (Hearing loss)","Disgenet (Mandibulofacial dysostosis)","CTD (Mandibulofacial dysostosis)","ClinVar (Treacher collins syndrome)","HPO (Treacher collins syndrome)","ClinGen (Treacher collins syndrome)","Orphanet (Treacher collins syndrome)"]
POLR3A	2	["Cerebellar ataxia","Hypomyelinating leukodystrophy"]	6	["RNA polymerase","Cytosolic DNA-sensing pathway","RNA Polymerase III Transcription Initiation From Type 3 Promoter","Cytosolic sensors of pathogen-associated DNA ","RNA Polymerase III Transcription Initiation From Type 1 Promoter","RNA Polymerase III Transcription Initiation From Type 2 Promoter"]	4	["Disgenet (Cerebellar ataxia)","Disgenet (Hypomyelinating leukodystrophy)","CTD (Hypomyelinating leukodystrophy)","HPO (Hypomyelinating leukodystrophy)"]

POLR1C (RNA polymerase I and III subunit C)

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