PNO1

partner of NOB1 homolog, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 2:68157888-68176238

Previous symbols: [ "KHRBP1" ]

Links

ENSG00000115946 ∙ NCBI:56902 ∙ OMIM:618710 ∙ HGNC:32790 ∙ Uniprot:Q9NRX1 ∙ 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 PNO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNO1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			30		1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	1

Variants in PNO1

This is a list of pathogenic ClinVar variants found in the PNO1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-68157949-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-68157950-G-C		not specified	Uncertain significance (Jan 30, 2024)
2-68157957-A-G		not specified	Uncertain significance (Sep 14, 2022)
2-68157958-G-C		not specified	Uncertain significance (Mar 07, 2023)
2-68157967-G-T		not specified	Uncertain significance (Dec 03, 2024)
2-68157977-G-T		not specified	Uncertain significance (Oct 01, 2024)
2-68157995-C-G		not specified	Uncertain significance (May 11, 2022)
2-68158073-A-G		not specified	Uncertain significance (Nov 14, 2024)
2-68158082-G-A		not specified	Uncertain significance (Jun 10, 2024)
2-68158106-C-G		not specified	Uncertain significance (Nov 30, 2021)
2-68158107-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-68158119-C-T		not specified	Uncertain significance (Jun 22, 2021)
2-68158125-G-A		not specified	Uncertain significance (Jan 03, 2022)
2-68158384-G-C			Benign (Dec 31, 2019)
2-68158392-G-A		not specified	Uncertain significance (Aug 17, 2022)
2-68158414-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-68158432-C-T		not specified	Uncertain significance (Nov 10, 2024)
2-68158458-T-C		not specified	Uncertain significance (Jul 09, 2024)
2-68158467-A-G		not specified	Uncertain significance (Dec 06, 2022)
2-68158500-A-G		not specified	Uncertain significance (Jan 16, 2024)
2-68162560-G-A		not specified	Uncertain significance (Jul 19, 2023)
2-68162571-A-G			Likely benign (Mar 05, 2018)
2-68162593-G-T		not specified	Uncertain significance (Oct 03, 2023)
2-68162615-A-C		not specified	Uncertain significance (Jun 28, 2022)
2-68162620-A-G		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNO1	protein_coding	protein_coding	ENST00000263657	7	18395

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.227	0.767	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.234	147	139	1.06	0.00000649	1638
Missense in Polyphen		33	41.817	0.78915		517
Synonymous	-0.445	54	50.0	1.08	0.00000233	502
Loss of Function	2.33	3	11.5	0.260	5.00e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000478	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA (PubMed:25851604). {ECO:0000269|PubMed:25851604}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.321
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.884
• hipred: Y
• hipred_score: 0.825
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pno1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol
• Molecular function: RNA binding