POP7

POP7 homolog, ribonuclease P/MRP subunit

Basic information

Region (hg38): 7:100706121-100707486

Links

ENSG00000172336 ∙ NCBI:10248 ∙ OMIM:606113 ∙ HGNC:19949 ∙ Uniprot:O75817 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POP7 gene.

• not_specified (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POP7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005837.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			22			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POP7	protein_coding	protein_coding	ENST00000303151	1	1443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0375	0.653	125729	0	7	125736	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.457	74	85.9	0.861	0.00000523	891
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

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.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.283
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.0887
• hipred: Y
• hipred_score: 0.614
• ghis: 0.545

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pop7

Gene ontology

• Biological process: tRNA 5'-leader removal;tRNA processing;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: ribonuclease MRP complex;nucleus;nucleoplasm;nucleolar ribonuclease P complex;cytoplasm;multimeric ribonuclease P complex
• Molecular function: RNA binding;ribonuclease P activity;protein binding