PIR

pirin

Basic information

Region (hg38): X:15384799-15493564

Links

ENSG00000087842

∙ NCBI:8544 ∙ OMIM:300931 ∙ HGNC:30048 ∙ Uniprot:O00625 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

complex neurodevelopmental disorder (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PIR gene.

not_specified (20 variants)
not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIR gene is commonly pathogenic or not. These statistics are base on transcript: NM_001018109.3. 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						0
missense			21 clinvar		4 clinvar	25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	4

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIR	protein_coding	protein_coding	ENST00000380421	9	108767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.34e-10	0.0336	125681	26	40	125747	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.398	119	107	1.11	0.00000789	1895
Missense in Polyphen		42	37.599	1.117		700
Synonymous	-0.0660	41	40.5	1.01	0.00000323	547
Loss of Function	-0.603	13	10.9	1.20	7.35e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000606	0.000570
Ashkenazi Jewish	0.00	0.00
East Asian	0.000290	0.000163
Finnish	0.000812	0.000601
European (Non-Finnish)	0.000247	0.000176
Middle Eastern	0.000290	0.000163
South Asian	0.000897	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional coregulator of NF-kappa-B which facilitates binding of NF-kappa-B proteins to target kappa-B genes in a redox-state-dependent manner. May be required for efficient terminal myeloid maturation of hematopoietic cells. Has quercetin 2,3-dioxygenase activity (in vitro). {ECO:0000269|PubMed:17288615, ECO:0000269|PubMed:20010624, ECO:0000269|PubMed:20711196, ECO:0000269|PubMed:23716661}.;
Pathway: y branching of actin filaments;Digestion;Digestion and absorption (Consensus)

Recessive Scores

pRec: 0.289

Intolerance Scores

loftool: 0.847
rvis_EVS: 0.48
rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

pHI: 0.144
hipred: N
hipred_score: 0.389
ghis: 0.437

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.792

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pir
Phenotype: growth/size/body region phenotype; embryo phenotype;

Gene ontology

Biological process: transcription by RNA polymerase II;digestion;monocyte differentiation;oxidation-reduction process;regulation of nucleic acid-templated transcription
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
Molecular function: transcription coregulator activity;protein binding;quercetin 2,3-dioxygenase activity;metal ion binding