PTCD1 pentatricopeptide repeat domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTCD1provided by HGNC
Official Full Name: pentatricopeptide repeat domain 1provided by HGNC
Primary source: HGNC:HGNC:22198
See related: Ensembl:ENSG00000106246 MIM:614774; AllianceGenome:HGNC:22198
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This gene encodes a mitochondrial protein that binds leucine tRNAs and other mitochondrial RNAs and plays a role in the regulation of translation. Increased expression of this gene results in decreased mitochondrial leucine tRNA levels. Naturally occurring read-through transcription exists between upstream ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and this gene. [provided by RefSeq, Aug 2015]
Expression: Ubiquitous expression in testis (RPKM 5.8), bone marrow (RPKM 4.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q22.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (99416739..99438798, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (100655640..100677699, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (99014362..99036421, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

reduced PTCD1 activity disrupts neuronal energy homeostasis and dampens spontaneous neural transmission in Alzheimer's Disease
Title: PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease.
Leucine starvation decreased PTCD1 on the protein level.
Title: Mitochondrial leucine tRNA level and PTCD1 are regulated in response to leucine starvation.
ELAC2 and PTCD1 affect the 3' end processing of tRNAs.
Title: RNA processing in human mitochondria.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

D8S2279 (e-PCR)
- UniSTS:473907

D15S1477 (e-PCR)
- UniSTS:474482

D11S3114 (e-PCR)
- UniSTS:152207

SHGC-58489 (e-PCR)
- UniSTS:94364

NoName (e-PCR)
- UniSTS:483010

D5S1597E (e-PCR)
- UniSTS:151019

Readthrough ATP5MF-PTCD1

Readthrough gene: ATP5MF-PTCD1, Included gene: ATP5MF

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables tRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables tRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in mitochondrial translation	IEA Inferred from Electronic Annotation more info
involved_in tRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA 3'-end processing	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in mitochondrial matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrial matrix	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: pentatricopeptide repeat-containing protein 1, mitochondrial

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_042827.1 RefSeqGene

Range

5042..27101

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_015545.4 → NP_056360.2 pentatricopeptide repeat-containing protein 1, mitochondrial

See identical proteins and their annotated locations for NP_056360.2

Status: REVIEWED

Source sequence(s)

AB014532, DA770648

Consensus CDS

CCDS34691.1

UniProtKB/Swiss-Prot

O75127, Q3ZB78, Q66K60, Q9UDV2

UniProtKB/TrEMBL

A4D273, Q3ZB84

Related

ENSP00000292478.5, ENST00000292478.9

Conserved Domains (3) summary

TIGR00756
Location:176 → 208

PPR; pentatricopeptide repeat domain (PPR motif)

sd00004
Location:176 → 202

PPR; PPR repeat [structural motif]

pfam13041
Location:553 → 596

PPR_2; PPR repeat family