PTRHD1

peptidyl-tRNA hydrolase domain containing 1

Basic information

Region (hg38): 2:24789728-24793391

Previous symbols: [ "C2orf79" ]

Links

ENSG00000184924 ∙ NCBI:391356 ∙ OMIM:617342 ∙ HGNC:33782 ∙ Uniprot:Q6GMV3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	AR	Neurologic	Individuals have been described as responding to levodopa	Neurologic	27134041; 27753167; 30398675; 38346691

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTRHD1 gene.

• Parkinsonian disorder (1 variants)
• Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTRHD1 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				3		3
missense	1		6		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	1	0	6	3	2

Variants in PTRHD1

This is a list of pathogenic ClinVar variants found in the PTRHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-24790469-C-T		Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Uncertain significance (Mar 17, 2024)
2-24790470-G-A		Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (May 07, 2024)
2-24790502-T-G		not specified	Uncertain significance (Sep 01, 2021)
2-24790533-T-C		not specified • PTRHD1-related disorder	Uncertain significance (Apr 27, 2023)
2-24790549-G-A		PTRHD1-related disorder	Likely benign (Jan 28, 2020)
2-24790654-G-C			Benign (May 14, 2021)
2-24793181-GGGTGGTCGCGGTGAGTGTGCAAGGCCGC-G		Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (Mar 13, 2024)
2-24793188-C-G		not specified	Uncertain significance (Mar 02, 2023)
2-24793189-G-A		PTRHD1-related disorder	Likely benign (Aug 28, 2019)
2-24793221-G-A		Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (Mar 13, 2024)
2-24793223-C-T		Parkinsonian disorder • Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (Dec 14, 2021)
2-24793237-C-G		PTRHD1-related disorder	Likely benign (Aug 13, 2019)
2-24793245-C-T		not specified	Uncertain significance (Mar 18, 2024)
2-24793251-G-T		PTRHD1-related disorder	Benign (Jun 14, 2019)
2-24793296-A-G		not specified	Uncertain significance (Feb 21, 2024)
2-24793336-C-G		PTRHD1-related disorder	Uncertain significance (Feb 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTRHD1	protein_coding	protein_coding	ENST00000328379	2	3649

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.62e-7	0.0673	125677	0	70	125747	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.192	89	84.1	1.06	0.00000407	891
Missense in Polyphen		28	29.07	0.96319		342
Synonymous	-1.19	47	37.7	1.25	0.00000187	300
Loss of Function	-1.22	8	5.04	1.59	2.24e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00185	0.00183
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000164	0.000163
South Asian	0.000328	0.000327
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.282
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptrhd1

Gene ontology

• Molecular function: aminoacyl-tRNA hydrolase activity