PTCD3

pentatricopeptide repeat domain 3, the group of Small nucleolar RNA protein coding host genes|Pentatricopeptide repeat containing

Basic information

Region (hg38): 2:86106223-86142157

Links

ENSG00000132300 ∙ NCBI:55037 ∙ OMIM:614918 ∙ HGNC:24717 ∙ Uniprot:Q96EY7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 51 (Strong), mode of inheritance: AR
• combined oxidative phosphorylation deficiency 51 (Moderate), mode of inheritance: AR
• Leigh syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 51	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Biochemical; Neurologic; Ophthalmologic	30607703; 30706245

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTCD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCD3 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	1	3
missense			47	3	1	51
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			1	2		3
non coding						0
Total	0	4	48	4	2

Variants in PTCD3

This is a list of pathogenic ClinVar variants found in the PTCD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-86106252-C-T			Benign (May 22, 2021)
2-86106254-G-A		Inborn genetic diseases	Uncertain significance (Sep 21, 2021)
2-86106264-C-T		Inborn genetic diseases	Uncertain significance (Mar 31, 2022)
2-86106278-G-T		PTCD3-related disorder	Likely benign (May 31, 2023)
2-86106281-C-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
2-86106285-G-C		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
2-86106287-A-C		Inborn genetic diseases	Uncertain significance (Jan 19, 2024)
2-86106306-T-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
2-86106318-G-A		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
2-86106333-A-T		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
2-86108536-G-C		Combined oxidative phosphorylation deficiency 51	Uncertain significance (Aug 09, 2021)
2-86111126-G-A			Likely benign (Aug 01, 2024)
2-86111150-G-C		Inborn genetic diseases	Uncertain significance (Apr 22, 2022)
2-86111154-A-G		Inborn genetic diseases	Uncertain significance (Dec 17, 2023)
2-86116578-C-T		Inborn genetic diseases	Uncertain significance (May 30, 2024)
2-86117056-G-A		Inborn genetic diseases	Likely benign (Feb 28, 2023)
2-86117158-C-T		Inborn genetic diseases	Uncertain significance (Aug 22, 2023)
2-86118919-A-G		Combined oxidative phosphorylation deficiency 51	Pathogenic (Feb 08, 2024)
2-86118927-A-T		Inborn genetic diseases	Uncertain significance (Apr 08, 2024)
2-86118942-G-A		Inborn genetic diseases	Uncertain significance (Jan 16, 2024)
2-86118952-T-G			Uncertain significance (Sep 01, 2023)
2-86121500-C-T		Inborn genetic diseases	Uncertain significance (May 02, 2024)
2-86121530-A-G		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
2-86121556-G-T		Inborn genetic diseases	Uncertain significance (May 28, 2024)
2-86121598-A-G		PTCD3-related disorder	Likely benign (Mar 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCD3	protein_coding	protein_coding	ENST00000254630	24	35976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.49e-22	0.0241	125644	0	104	125748	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.480	394	368	1.07	0.0000181	4559
Missense in Polyphen		81	85.775	0.94433		1134
Synonymous	-0.714	138	128	1.08	0.00000646	1229
Loss of Function	1.10	38	46.1	0.825	0.00000238	551

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00108	0.00107
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000385	0.000381
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000471	0.000466
Middle Eastern	0.000385	0.000381
South Asian	0.000168	0.000163
Other	0.000828	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial RNA-binding protein that has a role in mitochondrial translation. {ECO:0000269|PubMed:19427859}.
• Pathway: Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0835

Intolerance Scores

• loftool: 0.941
• rvis_EVS: -0.57
• rvis_percentile_EVS: 19.01

Haploinsufficiency Scores

• pHI: 0.0490
• hipred: N
• hipred_score: 0.266
• ghis: 0.562

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptcd3

Gene ontology

• Biological process: regulation of translation;mitochondrial translation;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: nucleoplasm;mitochondrion;mitochondrial inner membrane;cytosol;ribosome;plasma membrane
• Molecular function: RNA binding;protein binding;rRNA binding;ribosomal small subunit binding