PPIL6

protein-coding

peptidylprolyl isomerase like 6, the group of Cyclophilin peptidylprolyl isomerases

Gene summary

Predicted to enable peptidyl-prolyl cis-trans isomerase activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_173672.5

Inheritance

—

ClinVar variants

U:54B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr6:109,390,215-109,441,171

External References & Databases

Ensembl (ENSG00000185250)

Transcript & Mutation Effects

hg38 • Region Span ~51.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPIL6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173672.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			52 clinvar	4 clinvar		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	54	4	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173672.5	RefSeq	NP_775943.1	8	MANE Select
ENST00000521072.7	Ensembl	ENSP00000427929.1	8	MANE Select
NM_001111298.2	RefSeq	NP_001104768.2	9	Standard
NM_001286360.1	RefSeq	NP_001273289.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
mRNA Splicing - Major Pathway
mRNA Splicing
Processing of Capped Intron-Containing Pre-mRNA

Biological Process

protein peptidyl-prolyl isomerization
protein refolding

Molecular Function

peptidyl-prolyl cis-trans isomerase activity
cyclosporin A binding
unfolded protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000440797
Coding exons: 9
Length: 50957
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 55
Defined: 125746
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.241	175	166	1.05	0.00000815	2201
Missense (PolyPhen)		77	68.878	1.1179		899
Synonymous	0.530	54	59.2	0.912	0.00000306	617
Loss of Function	0.598	15	17.7	0.847	8.81e-7	221

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00055	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00029	0.00026	rare
South Asian	0.00015	0.00013	rare
Other	0.00061	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable inactive PPIase with no peptidyl-prolyl cis- trans isomerase activity. {ECO:0000269|PubMed:20676357}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.935
RVIS EVS: -0.25
RVIS percentile EVS: 35.75

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.415

Gene Damage Prediction

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