PIN4

peptidylprolyl cis/trans isomerase, NIMA-interacting 4, the group of Parvulins

Basic information

Region (hg38): X:72181352-72302926

Links

ENSG00000102309 ∙ NCBI:5303 ∙ OMIM:300252 ∙ HGNC:8992 ∙ Uniprot:Q9Y237 ∙ 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 PIN4 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIN4 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	6	0	0

Variants in PIN4

This is a list of pathogenic ClinVar variants found in the PIN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-72181741-G-A		not specified	Uncertain significance (Jan 30, 2024)
X-72181744-C-G		not specified	Uncertain significance (Sep 17, 2021)
X-72181765-G-C		not specified	Uncertain significance (Mar 06, 2023)
X-72181784-A-G		not specified	Uncertain significance (Dec 12, 2023)
X-72181798-G-A		not specified	Uncertain significance (Oct 26, 2021)
X-72181819-G-A		not specified	Uncertain significance (Mar 14, 2023)
X-72197408-C-A		not specified	Uncertain significance (Apr 07, 2022)
X-72197476-G-A		not specified	Uncertain significance (Sep 14, 2023)
X-72205067-G-A		not specified	Uncertain significance (Aug 15, 2023)
X-72205274-G-A		not specified	Uncertain significance (Oct 16, 2023)
X-72205325-C-T			Likely benign (-)
X-72205359-G-A			Likely benign (Mar 01, 2023)
X-72205470-A-T			Likely benign (Jul 01, 2022)
X-72205611-T-A		not specified	Uncertain significance (Feb 13, 2023)
X-72205942-G-T		not specified	Uncertain significance (Feb 07, 2023)
X-72205954-AACTTGGCCTC-A		not specified	Uncertain significance (Nov 17, 2016)
X-72206057-C-G		not specified	Uncertain significance (Jan 23, 2023)
X-72206081-A-C		not specified	Uncertain significance (Oct 04, 2022)
X-72206108-C-T		not specified	Uncertain significance (Sep 16, 2021)
X-72206231-C-G		not specified	Uncertain significance (Dec 19, 2022)
X-72206248-T-C		not specified	Uncertain significance (Mar 08, 2024)
X-72206437-A-G		not specified	Uncertain significance (Oct 03, 2022)
X-72206450-C-T		not specified	Uncertain significance (Jul 26, 2022)
X-72206509-T-C		not specified	Uncertain significance (Dec 05, 2022)
X-72206930-T-C		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIN4	protein_coding	protein_coding	ENST00000373669	4	121574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.713	0.274	125725	1	1	125727	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.122	60	57.4	1.05	0.00000385	1027
Missense in Polyphen		7	14.618	0.47887		298
Synonymous	-1.31	27	19.6	1.38	0.00000137	288
Loss of Function	1.88	0	4.11	0.00	2.59e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000366	0.0000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1 is involved as a ribosomal RNA processing factor in ribosome biogenesis. Binds to tightly bent AT-rich stretches of double-stranded DNA. {ECO:0000269|PubMed:19369196}.
• Pathway: Fibroblast growth factor-1 (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• loftool: 0.102
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.22

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.276
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pin4

Gene ontology

• Biological process: protein peptidyl-prolyl isomerization
• Cellular component: nucleus;nucleolus;mitochondrial matrix;spindle
• Molecular function: DNA binding;RNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding