PTRH1

peptidyl-tRNA hydrolase 1 homolog

Basic information

Region (hg38): 9:127690347-127724873

Previous symbols: [ "C9orf115" ]

Links

ENSG00000187024 ∙ NCBI:138428 ∙ ∙ HGNC:27039 ∙ Uniprot:Q86Y79 ∙ 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 PTRH1 gene.

• Inborn genetic diseases (39 variants)
• not provided (15 variants)
• Developmental and epileptic encephalopathy, 4 (1 variants)
• Non-syndromic intellectual disability (1 variants)
• Early Infantile Epileptic Encephalopathy, Autosomal Dominant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTRH1 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	1			1		2
missense		2	14	1	1	18
nonsense						0
start loss						0
frameshift	1					1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			28	5	1	34
Total	2	2	42	8	2

Variants in PTRH1

This is a list of pathogenic ClinVar variants found in the PTRH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127690513-G-A			Likely benign (Jun 14, 2018)
9-127690612-C-T			Likely benign (Jun 14, 2018)
9-127690673-T-C			Likely benign (Jan 18, 2021)
9-127690698-T-C			Benign (Jun 29, 2018)
9-127690778-C-T		Non-syndromic intellectual disability	Likely pathogenic (Jan 06, 2017)
9-127690779-C-T			Benign (Mar 03, 2015)
9-127690781-C-T			Likely pathogenic (Nov 18, 2021)
9-127690788-C-G		Developmental and epileptic encephalopathy, 4	Likely benign (May 06, 2021)
9-127690797-AC-A			Pathogenic (Mar 14, 2013)
9-127690798-C-T			Pathogenic (May 06, 2022)
9-127690804-C-G			Uncertain significance (Apr 20, 2022)
9-127690835-C-T		Inborn genetic diseases	Uncertain significance (Jun 26, 2017)
9-127690839-T-A			Uncertain significance (Nov 14, 2019)
9-127690849-A-C			Uncertain significance (Oct 07, 2019)
9-127690855-TA-T			Likely benign (Feb 26, 2021)
9-127691665-CAGTT-C		Early Infantile Epileptic Encephalopathy, Autosomal Dominant	Likely benign (Jun 14, 2016)
9-127695053-TTGATGATGATGA-T			Likely benign (Oct 01, 2023)
9-127695080-A-G			Likely benign (Jul 01, 2023)
9-127707041-A-C		not specified	Uncertain significance (Oct 20, 2023)
9-127707183-G-T		not specified	Uncertain significance (Nov 09, 2023)
9-127707191-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-127709544-T-G		not specified	Uncertain significance (Oct 12, 2021)
9-127709552-A-C		not specified	Uncertain significance (Jan 17, 2024)
9-127709567-G-A		not specified	Uncertain significance (Mar 13, 2023)
9-127709574-T-C		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTRH1	protein_coding	protein_coding	ENST00000419060	5	31896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000168	0.465	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0321	125	124	1.01	0.00000679	1312
Missense in Polyphen		37	43.494	0.85068		477
Synonymous	-0.435	61	56.8	1.07	0.00000309	491
Loss of Function	0.288	6	6.81	0.881	2.93e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.000687	0.000686
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.326

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.296
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptrh1

Gene ontology

• Molecular function: RNA binding;aminoacyl-tRNA hydrolase activity;protein binding