PIWIL3

piwi like RNA-mediated gene silencing 3, the group of Piwi like RNA-mediated gene silencing family

Basic information

Region (hg38): 22:24719033-24774720

Links

ENSG00000184571 ∙ NCBI:440822 ∙ OMIM:610314 ∙ HGNC:18443 ∙ Uniprot:Q7Z3Z3 ∙ 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 PIWIL3 gene.

• Inborn genetic diseases (43 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIWIL3 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			40	6	3	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	6	4

Variants in PIWIL3

This is a list of pathogenic ClinVar variants found in the PIWIL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-24719489-G-A			Benign (Mar 29, 2018)
22-24719519-G-T		not specified	Uncertain significance (Aug 06, 2021)
22-24719573-G-C		not specified	Uncertain significance (Nov 30, 2022)
22-24719782-G-A		not specified	Uncertain significance (Sep 16, 2021)
22-24719788-C-T		not specified	Uncertain significance (Dec 03, 2021)
22-24719789-G-A		not specified	Uncertain significance (Sep 27, 2021)
22-24719813-C-T		not specified	Uncertain significance (Dec 02, 2022)
22-24719831-C-T		not specified	Uncertain significance (Aug 23, 2021)
22-24719883-A-C		not specified	Uncertain significance (Dec 13, 2021)
22-24723193-C-T		not specified	Uncertain significance (Feb 28, 2023)
22-24723214-G-A		not specified	Uncertain significance (Dec 27, 2023)
22-24723244-G-T		not specified	Uncertain significance (Jun 12, 2023)
22-24724919-C-T		not specified	Uncertain significance (Dec 15, 2022)
22-24725004-G-A		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
22-24725512-C-G		not specified	Uncertain significance (Mar 16, 2022)
22-24727968-G-A		not specified	Likely benign (Jan 23, 2023)
22-24728192-C-G		not specified	Uncertain significance (Mar 28, 2023)
22-24728320-A-G		not specified	Uncertain significance (Feb 16, 2023)
22-24728340-C-T		not specified	Uncertain significance (Nov 08, 2022)
22-24728343-C-T		not specified	Likely benign (Oct 12, 2022)
22-24728348-G-T		not specified	Uncertain significance (Jan 02, 2024)
22-24734100-C-A		not specified	Uncertain significance (Jan 04, 2024)
22-24734110-T-C		not specified	Uncertain significance (Aug 08, 2022)
22-24734113-G-A		not specified	Uncertain significance (Apr 13, 2023)
22-24734125-T-C		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIWIL3	protein_coding	protein_coding	ENST00000332271	20	55687

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.35e-32	0.0000662	123424	7	2317	125748	0.00928

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0134	499	498	1.00	0.0000276	5744
Missense in Polyphen		121	142.25	0.85059		1783
Synonymous	0.337	172	178	0.968	0.00000983	1667
Loss of Function	0.235	49	50.8	0.964	0.00000275	599

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0249	0.0249
Ashkenazi Jewish	0.00248	0.00248
East Asian	0.00773	0.00775
Finnish	0.00213	0.00213
European (Non-Finnish)	0.0108	0.0108
Middle Eastern	0.00773	0.00775
South Asian	0.00705	0.00695
Other	0.0104	0.0103

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Directly binds piRNAs, a class of 24 to 30 nucleotide RNAs that are generated by a Dicer-independent mechanism and are primarily derived from transposons and other repeated sequence elements. Besides their function in transposable elements repression, piRNAs are probably involved in other processes during meiosis such as translation regulation (By similarity). {ECO:0000250|UniProtKB:Q9JMB7}.

Recessive Scores

• pRec: 0.0854

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 2.43
• rvis_percentile_EVS: 98.54

Haploinsufficiency Scores

• pHI: 0.0905
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of translation;multicellular organism development;spermatogenesis;cell differentiation;gene silencing by RNA;meiotic cell cycle
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding