PTER

phosphotriesterase related

Basic information

Region (hg38): 10:16436942-16513745

Links

ENSG00000165983 ∙ NCBI:9317 ∙ OMIM:604446 ∙ HGNC:9590 ∙ Uniprot:Q96BW5 ∙ 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 PTER gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTER 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					2	2
missense			27	1	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	3

Variants in PTER

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

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

Position	Type	Phenotype	Significance	ClinVar
10-16484398-G-C		not specified	Uncertain significance (Dec 15, 2023)
10-16484449-G-A		not specified	Uncertain significance (Jun 24, 2022)
10-16484468-C-A		not specified	Uncertain significance (Mar 01, 2024)
10-16484486-C-A		not specified	Uncertain significance (Apr 05, 2023)
10-16484500-C-T		not specified	Uncertain significance (Jun 30, 2023)
10-16484555-A-G			Benign (Mar 05, 2018)
10-16484618-A-T		not specified	Uncertain significance (Mar 01, 2023)
10-16484748-A-G		not specified	Uncertain significance (Oct 06, 2021)
10-16484760-G-A		not specified	Uncertain significance (Oct 12, 2021)
10-16484761-G-T		not specified	Uncertain significance (Jul 12, 2023)
10-16484773-A-T		not specified	Uncertain significance (May 26, 2024)
10-16484796-A-T		not specified	Uncertain significance (Mar 16, 2022)
10-16486355-A-G			Benign (Jun 14, 2018)
10-16486361-G-T		not specified	Uncertain significance (Apr 05, 2023)
10-16486365-T-C		not specified	Uncertain significance (Sep 16, 2021)
10-16486478-A-G		not specified	Uncertain significance (Aug 02, 2021)
10-16486515-T-C		not specified	Uncertain significance (Jul 05, 2023)
10-16486521-A-T		not specified	Uncertain significance (May 08, 2023)
10-16486529-C-T			Likely benign (Aug 09, 2017)
10-16486565-T-A		not specified	Uncertain significance (Dec 21, 2023)
10-16486579-C-T			Benign (Jun 14, 2018)
10-16486607-C-T		not specified	Uncertain significance (Jan 16, 2024)
10-16505025-T-C		not specified	Uncertain significance (Apr 20, 2023)
10-16505033-A-G		not specified	Uncertain significance (Mar 07, 2024)
10-16505061-T-C		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTER	protein_coding	protein_coding	ENST00000378000	4	76795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-13	0.00600	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.643	221	196	1.13	0.0000102	2282
Missense in Polyphen		89	73.396	1.2126		895
Synonymous	0.453	69	74.0	0.933	0.00000413	692
Loss of Function	-0.932	17	13.3	1.28	7.97e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000666
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000598	0.000598
South Asian	0.00137	0.00137
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.810

Intolerance Scores

• loftool: 0.961
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.466
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pter

Gene ontology

• Biological process: catabolic process;epithelial cell differentiation
• Cellular component: extracellular exosome
• Molecular function: molecular_function;zinc ion binding;hydrolase activity, acting on ester bonds