PTGES3L-AARSD1

PTGES3L-AARSD1 readthrough

Basic information

Region (hg38): 17:42950525-42980528

Links

ENSG00000108825 ∙ NCBI:100885850 ∙ ∙ HGNC:43946 ∙ Uniprot:Q9BTE6 ∙ 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 PTGES3L-AARSD1 gene.

• Inborn genetic diseases (26 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTGES3L-AARSD1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1	1	3
Total	0	0	25	2	1

Variants in PTGES3L-AARSD1

This is a list of pathogenic ClinVar variants found in the PTGES3L-AARSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42950612-G-A		not specified	Uncertain significance (Mar 22, 2022)
17-42950613-T-C		not specified	Uncertain significance (Jun 10, 2022)
17-42950636-G-A		not specified	Uncertain significance (Jul 20, 2022)
17-42950649-T-G		not specified	Uncertain significance (Dec 09, 2023)
17-42950655-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-42950672-T-A		not specified	Uncertain significance (Sep 29, 2023)
17-42950685-G-A		not specified	Uncertain significance (Jul 14, 2021)
17-42950728-C-G		not specified	Uncertain significance (Jun 29, 2023)
17-42951854-C-A		not specified	Uncertain significance (Jan 11, 2023)
17-42951854-C-G		not specified	Likely benign (Feb 17, 2024)
17-42951879-A-C		not specified	Uncertain significance (Dec 28, 2022)
17-42953740-T-C		not specified	Uncertain significance (Oct 12, 2022)
17-42954888-A-G		not specified	Uncertain significance (Feb 15, 2023)
17-42954895-C-T		not specified	Uncertain significance (Dec 09, 2023)
17-42954900-C-A		not specified	Uncertain significance (Jun 01, 2023)
17-42954924-T-C		not specified	Uncertain significance (Oct 10, 2023)
17-42954943-G-C		not specified	Uncertain significance (Jun 21, 2023)
17-42955851-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-42956232-G-C		not specified	Uncertain significance (Aug 02, 2021)
17-42956286-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-42956310-C-T		not specified	Uncertain significance (May 31, 2023)
17-42956415-C-T		not specified	Uncertain significance (Feb 14, 2024)
17-42956499-C-T		not specified	Uncertain significance (Dec 21, 2022)
17-42957163-G-T		not specified	Uncertain significance (May 18, 2022)
17-42961203-T-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTGES3L-AARSD1	protein_coding	protein_coding	ENST00000421990	17	30003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.94e-9	0.963	125458	0	290	125748	0.00115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.222	331	343	0.966	0.0000193	3866
Missense in Polyphen		99	120.12	0.82419		1332
Synonymous	0.127	126	128	0.986	0.00000700	1124
Loss of Function	2.10	19	31.8	0.598	0.00000144	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00779	0.00781
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000449	0.000448
Middle Eastern	0.000381	0.000381
South Asian	0.00274	0.00275
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in trans to edit the amino acid moiety from incorrectly charged tRNA(Ala). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.112
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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