PTCD1

pentatricopeptide repeat domain 1, the group of Pentatricopeptide repeat containing

Basic information

Region (hg38): 7:99416739-99466163

Links

ENSG00000106246 ∙ NCBI:26024 ∙ OMIM:614774 ∙ HGNC:22198 ∙ Uniprot:O75127 ∙ 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 PTCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTCD1 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	4	5
missense			58	12	2	72
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	62	13	6

Variants in PTCD1

This is a list of pathogenic ClinVar variants found in the PTCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99417522-G-C		not specified	Uncertain significance (Apr 18, 2023)
7-99417572-G-A		not specified	Uncertain significance (Dec 22, 2023)
7-99419434-C-G		not specified	Uncertain significance (Jun 12, 2023)
7-99419979-A-G			Likely benign (Dec 01, 2022)
7-99419986-C-T		not specified	Uncertain significance (Dec 21, 2023)
7-99419990-C-G		not specified	Likely benign (Apr 12, 2024)
7-99419990-C-T		not specified	Likely benign (Oct 03, 2022)
7-99420000-C-G		not specified	Uncertain significance (Jun 24, 2022)
7-99420058-G-A		not specified	Likely benign (Dec 06, 2022)
7-99420071-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-99420092-G-A			Uncertain significance (Feb 02, 2016)
7-99420136-T-C		not specified	Uncertain significance (Oct 26, 2022)
7-99423814-C-A		not specified	Uncertain significance (Nov 30, 2022)
7-99423818-C-T		not specified	Uncertain significance (Jan 10, 2022)
7-99423843-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-99423909-C-T		not specified	Uncertain significance (Jan 08, 2024)
7-99423912-T-A		not specified	Uncertain significance (May 30, 2023)
7-99423950-T-G		not specified	Uncertain significance (Mar 31, 2023)
7-99424829-G-A		not specified	Uncertain significance (Apr 18, 2023)
7-99424872-T-G		not specified	Uncertain significance (Oct 10, 2023)
7-99424901-G-A		not specified	Uncertain significance (Oct 26, 2022)
7-99424919-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-99424939-G-C		not specified	Uncertain significance (Jul 20, 2021)
7-99425006-G-A		not specified	Uncertain significance (May 08, 2023)
7-99425034-C-G		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTCD1	protein_coding	protein_coding	ENST00000555673	9	49426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.91e-14	0.134	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.560	466	433	1.08	0.0000283	4845
Missense in Polyphen		138	136.56	1.0106		1560
Synonymous	-2.09	234	197	1.19	0.0000139	1556
Loss of Function	0.924	24	29.4	0.816	0.00000162	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000508	0.000507
Ashkenazi Jewish	0.00	0.00
East Asian	0.000599	0.000598
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000328	0.000325
Middle Eastern	0.000599	0.000598
South Asian	0.000980	0.000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial protein implicated in negative regulation of leucine tRNA levels, as well as negative regulation of mitochondria-encoded proteins and COX activity. Affects also the 3'-processing of mitochondrial tRNAs. {ECO:0000269|PubMed:21857155}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 78.87

Haploinsufficiency Scores

• pHI: 0.0974
• hipred: N
• hipred_score: 0.146
• ghis: 0.402

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Mouse Genome Informatics

• Gene name: Ptcd1
• Phenotype: muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: tRNA 3'-end processing
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: tRNA binding;RNA binding