POLR1H

protein-coding

RNA polymerase I subunit H, the group of RNA polymerase subunits

Gene summary

This gene encodes a DNA-directed RNA polymerase I subunit. The encoded protein contains two potential zinc-binding motifs and may play a role in regulation of cell proliferation. The encoded protein may be involved in cancer and human immunodeficiency virus progression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Previous symbols:

ZNRD1

MANE transcript

NM_170783.4

Inheritance

—

ClinVar variants

U:9B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr6:30,058,899-30,064,909

External References & Databases

Ensembl (ENSG00000066379)

Transcript & Mutation Effects

hg38 • Region Span ~6.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to POLR1H variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_170783.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar	1 clinvar		10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	1	0	10

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_170783.4	RefSeq	NP_740753.1	4	MANE Select
ENST00000332435.10	Ensembl	ENSP00000331111.5	4	MANE Select
NM_001278785.2	RefSeq	NP_001265714.1	4	Standard
NM_001278786.2	RefSeq	NP_001265715.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyrimidine metabolism - Homo sapiens (human)
RNA polymerase - Homo sapiens (human)
Purine metabolism - Homo sapiens (human)
Pyrimidine metabolism
B-WICH complex positively regulates rRNA expression

Biological Process

nucleobase-containing compound metabolic process
transcription initiation from RNA polymerase I promoter
termination of RNA polymerase I transcription
mRNA cleavage
positive regulation of gene expression, epigenetic

Molecular Function

RNA polymerase I activity
nucleic acid binding
DNA-directed 5'-3' RNA polymerase activity
zinc ion binding

Cellular Component

nucleoplasm
RNA polymerase I complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332435
Coding exons: 4
Length: 6011
Individuals with no LoFs: 123669
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 123677
p: 0.0000323

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.00	52	76.8	0.677	0.00000383	827
Missense (PolyPhen)		12	29.303	0.40951		296
Synonymous	1.05	21	28.1	0.748	0.00000138	239
Loss of Function	1.73	2	6.90	0.290	3.60e-7	72

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000045	0.000045	rare
South Asian	0.000066	0.000066	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.;

Intolerance Scores

LoFtool: 0.505
RVIS EVS: 0.3
RVIS percentile EVS: 71.81

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.964

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium