PRUNE2

prune homolog 2 with BCH domain, the group of BCH domain containing

Basic information

Region (hg38): 9:76611376-76906114

Previous symbols: [ "C9orf65", "KIAA0367" ]

Links

ENSG00000106772 ∙ NCBI:158471 ∙ OMIM:610691 ∙ HGNC:25209 ∙ Uniprot:Q8WUY3 ∙ 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 PRUNE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRUNE2 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				9	8	17
missense			176	18	7	201
nonsense						0
start loss						0
frameshift						0
inframe indel					2	2
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	176	27	17

Variants in PRUNE2

This is a list of pathogenic ClinVar variants found in the PRUNE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-76619356-A-T		not specified	Uncertain significance (Feb 21, 2024)
9-76619368-C-G		not specified	Uncertain significance (Jan 06, 2023)
9-76629258-T-C		not specified	Likely benign (Sep 14, 2023)
9-76637419-G-A		not specified	Uncertain significance (Dec 08, 2023)
9-76637485-C-T		not specified	Uncertain significance (Mar 25, 2024)
9-76637506-T-C		not specified	Uncertain significance (Aug 04, 2022)
9-76638207-T-C		not specified	Uncertain significance (Feb 21, 2024)
9-76638210-T-C		not specified	Uncertain significance (Jan 22, 2024)
9-76638222-C-T		not specified	Uncertain significance (Jun 29, 2022)
9-76638226-T-G		not specified	Uncertain significance (May 30, 2024)
9-76638266-A-T		not specified	Uncertain significance (Mar 06, 2023)
9-76644742-C-T		not specified	Uncertain significance (Apr 27, 2024)
9-76644756-C-T		not specified	Uncertain significance (Sep 06, 2022)
9-76644826-G-C		not specified	Uncertain significance (Jun 29, 2023)
9-76652572-T-C		not specified	Uncertain significance (Feb 16, 2023)
9-76652647-G-C		not specified	Uncertain significance (Dec 17, 2021)
9-76655452-A-G		not specified	Uncertain significance (Oct 18, 2021)
9-76655459-C-T		not specified	Uncertain significance (Jul 26, 2021)
9-76655510-A-C			Benign (Feb 20, 2018)
9-76703397-G-A			Benign (May 08, 2018)
9-76703404-G-A		not specified	Uncertain significance (Jun 22, 2021)
9-76703437-G-C		not specified	Uncertain significance (Jan 02, 2024)
9-76703486-C-G			Benign (Feb 25, 2018)
9-76703487-G-A		not specified	Uncertain significance (Feb 17, 2022)
9-76703545-C-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRUNE2	protein_coding	protein_coding	ENST00000376718	19	294712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.96e-28	1.00	125185	1	562	125748	0.00224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.540	1534	1.59e+3	0.962	0.0000813	20440
Missense in Polyphen		383	441.2	0.86809		5831
Synonymous	-0.163	619	614	1.01	0.0000352	5858
Loss of Function	4.02	62	107	0.580	0.00000527	1406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00185	0.00179
Ashkenazi Jewish	0.00192	0.00179
East Asian	0.000891	0.000870
Finnish	0.00930	0.00914
European (Non-Finnish)	0.00210	0.00204
Middle Eastern	0.000891	0.000870
South Asian	0.00169	0.00157
Other	0.00205	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in regulating differentiation, survival and aggressiveness of the tumor cells. {ECO:0000269|PubMed:16288218}.

Recessive Scores

• pRec: 0.0780

Intolerance Scores

• loftool: 0.952
• rvis_EVS: 2.78
• rvis_percentile_EVS: 99.03

Haploinsufficiency Scores

• pHI: 0.0728
• hipred: N
• hipred_score: 0.280
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.334

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Prune2

Gene ontology

• Biological process: polyphosphate catabolic process;apoptotic process
• Cellular component: cytoplasm
• Molecular function: exopolyphosphatase activity;metal ion binding