POP7

protein-coding

POP7 homolog, ribonuclease P/MRP subunit

Gene summary

Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5'-leader removal. Located in nucleolus. Part of multimeric ribonuclease P complex and ribonuclease MRP complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_005837.3

Inheritance

—

ClinVar variants

U:23

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr7:100,706,121-100,707,486

External References & Databases

Ensembl (ENSG00000172336)

Transcript & Mutation Effects

hg38 • Region Span ~1.4 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 POP7 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 22

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005837.3. 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			1 clinvar			1
missense			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	0	0	23

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005837.3	RefSeq	NP_005828.2	1	MANE Select
ENST00000303151.5	Ensembl	ENSP00000304353.4	1	MANE Select
ENST00000457480.1	Ensembl	ENSP00000387814.1	1	Standard
ENST00000910791.1	Ensembl	ENSP00000580850.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
RNA transport - Homo sapiens (human)
tRNA processing
Metabolism of RNA
tRNA processing in the nucleus

Biological Process

tRNA 5'-leader removal
tRNA processing
RNA phosphodiester bond hydrolysis, endonucleolytic

Molecular Function

RNA binding
ribonuclease P activity
protein binding

Cellular Component

ribonuclease MRP complex
nucleus
nucleoplasm
nucleolar ribonuclease P complex
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000303151
Coding exons: 1
Length: 1443
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125736
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.457	74	85.9	0.861	0.00000523	891
Missense (PolyPhen)		15	23.655	0.63412		263
Synonymous	-0.0883	39	38.3	1.02	0.00000242	316
Loss of Function	0.408	2	2.73	0.733	1.22e-7	34

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
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)	0.000044	0.000044	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. Also a component of RNase MRP complex, which cleaves pre-rRNA sequences.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.283
RVIS EVS: 0.15
RVIS percentile EVS: 64.11

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.994

Gene Damage Prediction

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