PIWIL4

piwi like RNA-mediated gene silencing 4, the group of Piwi like RNA-mediated gene silencing family

Basic information

Region (hg38): 11:94543840-94621421

Links

ENSG00000134627

∙ NCBI:143689 ∙ OMIM:610315 ∙ HGNC:18444 ∙ Uniprot:Q7Z3Z4 ∙ 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 PIWIL4 gene.

not_specified (101 variants)
not_provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIWIL4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152431.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	2 clinvar	6
missense			94 clinvar	10 clinvar	2 clinvar	106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	94	14	4

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIWIL4	protein_coding	protein_coding	ENST00000299001	20	77582

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000183	1.00	125690	1	57	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	377	468	0.806	0.0000248	5578
Missense in Polyphen		79	109.26	0.72306		1269
Synonymous	1.14	151	170	0.889	0.00000911	1587
Loss of Function	3.79	18	45.6	0.395	0.00000217	562

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000383	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000383	0.000381
South Asian	0.000610	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity (By similarity). 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 governs the methylation and subsequent repression of transposons (By similarity). 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 (By similarity). Associates with secondary piRNAs antisense and PIWIL2/MILI is required for such association (By similarity). The piRNA process acts upstream of known mediators of DNA methylation (By similarity). Does not show endonuclease activity (By similarity). Plays a key role in the piRNA amplification loop, also named ping-pong amplification cycle, by acting as a 'slicer-incompetent' component that loads cleaved piRNAs from the 'slicer-competent' component PIWIL2 and target them on genomic transposon loci in the nucleus (By similarity). May be involved in the chromatin-modifying pathway by inducing 'Lys-9' methylation of histone H3 at some loci (PubMed:17544373). {ECO:0000250|UniProtKB:Q8CGT6, ECO:0000269|PubMed:17544373}.;
Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

pRec: 0.0924

Intolerance Scores

loftool: 0.789
rvis_EVS: 1.27
rvis_percentile_EVS: 93.63

Haploinsufficiency Scores

pHI: 0.0953
hipred: N
hipred_score: 0.322
ghis: 0.400

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.771

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Piwil4
Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: regulation of translation;multicellular organism development;spermatogenesis;negative regulation of transposition;epithelial structure maintenance;cell differentiation;gene silencing by RNA;piRNA metabolic process;DNA methylation involved in gamete generation;meiotic cell cycle;RNA phosphodiester bond hydrolysis, endonucleolytic
Cellular component: nucleus;cytoplasm;P granule;piP-body
Molecular function: endoribonuclease activity;piRNA binding