POP1 (POP1 ribonuclease P/MRP subunit)

Gene

• Entrez ID: 10940
• Gene name: POP1 ribonuclease P/MRP subunit
• Gene symbol: POP1
• Synonyms (NCBI Gene): ANXD2
• Chromosome: 8
• Chromosome location: 8q22.2
• Summary: This gene encodes the protein subunit of two different small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. The encoded protein is a ribonuclease that localizes to the n

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs374828868	G>A	Pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs769183311	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs1060505023	C>T	Pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant
rs1060505024	C>-	Pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1060505025	G>T	Pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT025418	hsa-miR-34a-5p	Proteomics	21566225
MIRT032295	hsa-let-7b-5p	Proteomics	18668040
MIRT044722	hsa-miR-320a	CLASH	23622248
MIRT512691	hsa-miR-4457	PAR-CLIP	23446348
MIRT512690	hsa-miR-125b-2-3p	PAR-CLIP	23446348
MIRT512689	hsa-miR-513b-5p	PAR-CLIP	23446348
MIRT512691	hsa-miR-4457	PAR-CLIP	23446348
MIRT512690	hsa-miR-125b-2-3p	PAR-CLIP	23446348
MIRT512689	hsa-miR-513b-5p	PAR-CLIP	23446348
MIRT1250150	hsa-miR-101	CLIP-seq
MIRT1250151	hsa-miR-128	CLIP-seq
MIRT1250152	hsa-miR-129-3p	CLIP-seq
MIRT1250153	hsa-miR-1324	CLIP-seq
MIRT1250154	hsa-miR-23a	CLIP-seq
MIRT1250155	hsa-miR-23b	CLIP-seq
MIRT1250156	hsa-miR-23c	CLIP-seq
MIRT1250157	hsa-miR-27a	CLIP-seq
MIRT1250158	hsa-miR-27b	CLIP-seq
MIRT1250159	hsa-miR-298	CLIP-seq
MIRT1250160	hsa-miR-3166	CLIP-seq
MIRT1250161	hsa-miR-3180-5p	CLIP-seq
MIRT1250162	hsa-miR-330-3p	CLIP-seq
MIRT1250163	hsa-miR-3622b-5p	CLIP-seq
MIRT1250164	hsa-miR-3668	CLIP-seq
MIRT1250165	hsa-miR-3684	CLIP-seq
MIRT1250166	hsa-miR-3688-3p	CLIP-seq
MIRT1250167	hsa-miR-375	CLIP-seq
MIRT1250168	hsa-miR-4270	CLIP-seq
MIRT1250169	hsa-miR-4304	CLIP-seq
MIRT1250170	hsa-miR-4422	CLIP-seq
MIRT1250171	hsa-miR-4441	CLIP-seq
MIRT1250172	hsa-miR-4685-5p	CLIP-seq
MIRT1250173	hsa-miR-4711-5p	CLIP-seq
MIRT1250174	hsa-miR-4717-3p	CLIP-seq
MIRT1250175	hsa-miR-515-5p	CLIP-seq
MIRT2073853	hsa-let-7a	CLIP-seq
MIRT2073854	hsa-let-7b	CLIP-seq
MIRT2073855	hsa-let-7c	CLIP-seq
MIRT2073856	hsa-let-7d	CLIP-seq
MIRT2073857	hsa-let-7e	CLIP-seq
MIRT2073858	hsa-let-7f	CLIP-seq
MIRT2073859	hsa-let-7g	CLIP-seq
MIRT2073860	hsa-let-7i	CLIP-seq
MIRT2073861	hsa-miR-2467-3p	CLIP-seq
MIRT2073862	hsa-miR-3678-3p	CLIP-seq
MIRT2073863	hsa-miR-4257	CLIP-seq
MIRT2073864	hsa-miR-4458	CLIP-seq
MIRT2073865	hsa-miR-4500	CLIP-seq
MIRT2073866	hsa-miR-4672	CLIP-seq
MIRT2073867	hsa-miR-98	CLIP-seq
MIRT1250164	hsa-miR-3668	CLIP-seq
MIRT1250174	hsa-miR-4717-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000172	Component	Ribonuclease MRP complex	IBA
GO:0000172	Component	Ribonuclease MRP complex	IDA	8918471, 16723659
GO:0000172	Component	Ribonuclease MRP complex	IEA
GO:0001682	Process	TRNA 5'-leader removal	IDA	16723659, 30454648
GO:0001682	Process	TRNA 5'-leader removal	IEA
GO:0003723	Function	RNA binding	HDA	22658674
GO:0003723	Function	RNA binding	IEA
GO:0004526	Function	Ribonuclease P activity	IDA	8918471, 30454648
GO:0004526	Function	Ribonuclease P activity	IEA
GO:0005515	Function	Protein binding	IPI	15096576, 28514442, 33961781
GO:0005615	Component	Extracellular space	HDA	22664934
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005655	Component	Nucleolar ribonuclease P complex	IBA
GO:0005655	Component	Nucleolar ribonuclease P complex	IDA	8918471
GO:0005655	Component	Nucleolar ribonuclease P complex	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0005730	Component	Nucleolus	IEA
GO:0008033	Process	TRNA processing	IBA
GO:0008033	Process	TRNA processing	IEA
GO:0016078	Process	TRNA decay	IDA	8918471
GO:0030681	Component	Multimeric ribonuclease P complex	IDA	16723659, 30454648
GO:0033204	Function	Ribonuclease P RNA binding	IDA	16723659, 30454648

Other IDs

• MIM: 602486
• HGNC: 30129
• e!Ensembl: ENSG00000104356

Protein

• UniProt ID: Q99575
• Protein name: Ribonucleases P/MRP protein subunit POP1 (hPOP1)
• Protein function: Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends (PubMed:30454648, PubMed:8918471). Also a component of the MRP ribonuclease complex, which cleaves pre-rRNA sequences (PubMed
• PDB: 6AHR, 6AHU
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF06978	POP1	107 → 190	Ribonucleases P/MRP protein subunit POP1	Family
  PF06978	POP1	168 → 258	Ribonucleases P/MRP protein subunit POP1	Family
  PF08170	POPLD	617 → 708	POPLD (NUC188) domain	Domain

• Sequence:

  MSNAKERKHAKKMRNQPTNVTLSSGFVADRGVKHHSGGEKPFQAQKQEPHPGTSRQRQTR
  VNPHSLPDPEVNEQSSSKGMFRKKGGWKAGPEGTSQEIPKYITASTFAQARAAEISAMLK
  AVTQKSSNSLVFQTLPRHMRRRAMSHNVKRLPRRLQEIAQKEAEKAVHQKKEHSKNKCHK
  ARRCHMNRTLEFNRRQKKNIWLETHIWHAKRFHMVKKWGYCLGERPTVKSHRACYRAMTN
  RCLLQDLSYYCCLELKGKEEEILKALSGMCNIDTGLTFAAVHCLSGKRQGSLVLYRVNKY
  PREMLGPVTFIWKSQRTPGDPSESRQLWIWLHPTLKQDILEEIKAACQCVEPIKSAVCIA
  DPLPTPSQEKSQTELPDEKIGKKRKRKDDGENAKPIKKIIGDGTRDPCLPYSWISPTTGI
  IISDLTMEMNRFRLIGPLSHSILTEAIKAASVHTVGEDTEETPHRWWIETCKKPDSVSLH
  CRQEAIFELLGGITSPAEIPAGTILGLTVGDPRINLPQKKSKALPNPEKCQDNEKVRQLL
  LEGVPVECTHSFIWNQDICKSVTENKISDQDLNRMRSELLVPGSQLILGPHESKIPILLI
  QQPGKVTGEDRLGWGSGWDVLLPKGWGMAFWIPFIYRGVRVGGLKESAVHSQYKRSPNVP
  GDFPDCPAGMLFAEEQAKNLLEKYKRRPPAKRPNYVKLGTLAPFCCPWEQLTQDWESRVQ
  AYEEPSVASSPNGKESDLRRSEVPCAPMPKKTHQPSDEVGTSIEHPREAEEVMDAGCQES
  AGPERITDQEASENHVAATGSHLCVLRSRKLLKQLSAWCGPSSEDSRGGRRAPGRGQQGL
  TREACLSILGHFPRALVWVSLSLLSKGSPEPHTMICVPAKEDFLQLHEDWHYCGPQESKH
  SDPFRSKILKQKEKKKREKRQKPGRASSDGPAGEEPVAGQEALTLGLWSGPLPRVTLHCS
  RTLLGFVTQGDFSMAVGCGEALGFVSLTGLLDMLSSQPAAQRGLVLLRPPASLQYRFARI
  AIEV

• Sequence length: 1024

Pathways

KEGG:

Ribosome biogenesis in eukaryotes

Reactome:

tRNA processing in the nucleus

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Anauxetic dysplasia 2	Likely pathogenic; Pathogenic	rs2130635894, rs1816281097, rs769183311, rs1060505023, rs1060505024, rs1060505025	RCV001806407 RCV003991791 RCV000445637 RCV000477695 RCV000477720 RCV000477675	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
POP1-related disorder	Likely pathogenic; Pathogenic	rs771454414	RCV003418872	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANAUXETIC DYSPLASIA	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANAUXETIC DYSPLASIA 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRION DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations