PPT2

palmitoyl-protein thioesterase 2

Basic information

Region (hg38): 6:32153440-32163678

Links

ENSG00000221988 ∙ NCBI:9374 ∙ OMIM:603298 ∙ HGNC:9326 ∙ Uniprot:Q9UMR5 ∙ 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 PPT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPT2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in PPT2

This is a list of pathogenic ClinVar variants found in the PPT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32154634-G-A		not specified	Likely benign (Oct 13, 2023)
6-32154686-C-T		not specified	Uncertain significance (Mar 19, 2024)
6-32154743-A-G		not specified	Uncertain significance (May 17, 2023)
6-32154758-T-A		not specified	Uncertain significance (Jan 03, 2024)
6-32155030-A-T		not specified	Uncertain significance (Mar 24, 2023)
6-32155045-G-C		not specified	Uncertain significance (Jun 03, 2022)
6-32155141-G-A		not specified	Uncertain significance (Apr 08, 2022)
6-32155151-C-T		not specified	Uncertain significance (Oct 12, 2022)
6-32155180-C-G		not specified	Uncertain significance (Jan 30, 2024)
6-32155693-C-A		not specified	Uncertain significance (Jun 02, 2023)
6-32155909-C-T		not specified	Uncertain significance (Jul 14, 2021)
6-32157648-G-A		not specified	Uncertain significance (Mar 15, 2024)
6-32157860-C-T		not specified	Uncertain significance (Jun 09, 2022)
6-32157917-C-G		not specified	Uncertain significance (Feb 17, 2022)
6-32162807-G-A		not specified	Uncertain significance (May 12, 2015)
6-32162817-G-C		not specified	Uncertain significance (Jun 12, 2023)
6-32162873-A-G		not specified	Uncertain significance (May 16, 2023)
6-32162909-C-G		not specified	Uncertain significance (Mar 28, 2024)
6-32162931-T-C		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPT2	protein_coding	protein_coding	ENST00000361568	9	12794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00454	0.989	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	108	187	0.578	0.0000102	2000
Missense in Polyphen		29	62.269	0.46572		687
Synonymous	1.96	55	76.9	0.715	0.00000404	621
Loss of Function	2.41	7	18.0	0.388	8.99e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000952	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000988	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Removes thioester-linked fatty acyl groups from various substrates including S-palmitoyl-CoA. Has the highest S- thioesterase activity for the acyl groups palmitic and myristic acid followed by other short- and long-chain acyl substrates. However, because of structural constraints, is unable to remove palmitate from peptides or proteins. {ECO:0000269|PubMed:10417332, ECO:0000269|PubMed:12855696, ECO:0000269|PubMed:9341199}.
• Pathway: Lysosome - Homo sapiens (human);Fatty acid elongation - Homo sapiens (human);Metabolism of lipids;Fatty acyl-CoA biosynthesis;Metabolism;Fatty acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.106
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.496
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppt2
• Phenotype: renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: fatty-acyl-CoA biosynthetic process;macromolecule depalmitoylation
• Cellular component: lysosome;lysosomal lumen;extracellular exosome
• Molecular function: palmitoyl-(protein) hydrolase activity;thiolester hydrolase activity;palmitoyl hydrolase activity