PTRH1

protein-coding

peptidyl-tRNA hydrolase 1 homolog

Gene summary

Enables peptidyl-tRNA hydrolase activity. Involved in rescue of stalled cytosolic ribosome. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C9orf115

MANE transcript

NM_001002913.3

Inheritance

—

ClinVar variants

U:50B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr9:127,690,348-127,724,873

External References & Databases

Ensembl (ENSG00000187024)

Transcript & Mutation Effects

hg38 • Region Span ~34.5 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 PTRH1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001002913.3. 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				1 clinvar		1
missense			50 clinvar	1 clinvar		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	2	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001002913.3	RefSeq	NP_001002913.1	5	MANE Select
ENST00000543175.5	Ensembl	ENSP00000439469.1	5	MANE Select
NM_001345977.1	RefSeq	NP_001332906.1	5	Standard
NM_001345978.1	RefSeq	NP_001332907.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase

Molecular Function

RNA binding
aminoacyl-tRNA hydrolase activity
protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419060
Coding exons: 5
Length: 31896
Individuals with no LoFs: 125704
Homozygous LoFs: 0
Heterozygous LoFs: 44
Defined: 125748
p: 0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0321	125	124	1.01	0.00000679	1312
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00069	0.00069	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.326

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: E
Indispensability score: 0.757

Gene Damage Prediction

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