PTCD2

Summary

PTCD2 (pentatricopeptide repeat domain 2, HGNC:25734) is a protein-coding gene on chromosome 5q13.2, encoding Pentatricopeptide repeat-containing protein 2, mitochondrial (Q8WV60). Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function.

Enables RNA binding activity. Predicted to be involved in mitochondrion organization and regulation of mRNA processing. Predicted to act upstream of or within several processes, including liver development; muscle cell development; and ventricular cardiac muscle tissue morphogenesis. Located in mitochondrion.

Source: NCBI Gene 79810 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_024754

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25734
Approved symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Location	5q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12598
Ensembl gene	ENSG00000049883
Ensembl biotype	protein_coding
OMIM	615484
Entrez	79810

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 5 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000308077, ENST00000380639, ENST00000460837, ENST00000486995, ENST00000493283, ENST00000503315, ENST00000503868, ENST00000510676, ENST00000511752, ENST00000515198, ENST00000536805, ENST00000543322, ENST00000866840, ENST00000926042

RefSeq mRNA: 4 — MANE Select: NM_024754 NM_001284403, NM_001284404, NM_001284405, NM_024754

CCDS: CCDS4014, CCDS68891, CCDS68892, CCDS75258

Canonical transcript exons

ENST00000380639 — 10 exons

Exon	Start	End
ENSE00001826712	72358203	72368395
ENSE00002112405	72320373	72320509
ENSE00003463433	72335018	72335096
ENSE00003466048	72352641	72352754
ENSE00003490850	72338622	72338735
ENSE00003529632	72331258	72331375
ENSE00003546653	72326612	72326741
ENSE00003575010	72322172	72322264
ENSE00003650147	72342962	72343036
ENSE00003680060	72335794	72335885

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 85.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5379 / max 156.1556, expressed in 1682 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
57000	6.5379	1682

Top tissues by expression

282 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
biceps brachii	UBERON:0001507	85.03	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	84.03	gold quality
corpus epididymis	UBERON:0004359	82.76	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.30	gold quality
endothelial cell	CL:0000115	82.19	silver quality
hindlimb stylopod muscle	UBERON:0004252	82.10	gold quality
calcaneal tendon	UBERON:0003701	81.05	gold quality
caput epididymis	UBERON:0004358	80.96	gold quality
muscle of leg	UBERON:0001383	80.32	gold quality
adrenal tissue	UBERON:0018303	80.18	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	80.09	gold quality
gastrocnemius	UBERON:0001388	80.04	gold quality
vastus lateralis	UBERON:0001379	80.02	silver quality
skeletal muscle organ	UBERON:0014892	79.52	gold quality
muscle organ	UBERON:0001630	79.51	gold quality
heart left ventricle	UBERON:0002084	79.41	gold quality
cardiac ventricle	UBERON:0002082	79.26	gold quality
cauda epididymis	UBERON:0004360	79.15	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.13	gold quality
ventricular zone	UBERON:0003053	79.09	gold quality
right adrenal gland cortex	UBERON:0035827	78.58	gold quality
right adrenal gland	UBERON:0001233	78.37	gold quality
heart right ventricle	UBERON:0002080	78.23	gold quality
prefrontal cortex	UBERON:0000451	78.12	gold quality
stromal cell of endometrium	CL:0002255	78.01	gold quality
cerebellar vermis	UBERON:0004720	77.65	silver quality
quadriceps femoris	UBERON:0001377	77.64	silver quality
left adrenal gland	UBERON:0001234	77.25	gold quality
heart	UBERON:0000948	77.20	gold quality
corpus callosum	UBERON:0002336	77.11	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting PTCD2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4762-5P	99.57	68.54	1424
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-642A-3P	99.23	67.67	1258
HSA-MIR-642B-3P	99.23	67.67	1258
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-1265	98.36	66.46	598
HSA-MIR-224-5P	98.33	70.12	1256
HSA-MIR-4768-3P	98.16	66.02	2330
HSA-MIR-3680-5P	98.06	66.20	394
HSA-MIR-6502-3P	97.86	65.43	569
HSA-MIR-203B-3P	97.82	66.27	979
HSA-MIR-4786-5P	97.45	67.89	924
HSA-MIR-6500-3P	97.42	67.20	867

Literature-anchored findings (GeneRIF, showing 1)

• Pentatricopeptide Protein PTCD2 Regulates COIII Translation in Mitochondria of the HeLa Cell Line. (PMID:36430722)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ptcd2	ENSDARG00000035391
mus_musculus	Ptcd2	ENSMUSG00000021650
rattus_norvegicus	Ptcd2	ENSRNOG00000028403

Protein

Protein identifiers

Pentatricopeptide repeat-containing protein 2, mitochondrial — Q8WV60 (reviewed: Q8WV60)

All UniProt accessions (7): B7Z8R2, D6RGK0, D6RIZ0, Q8WV60, D6RJH8, E5RHU2, F6S289

UniProt curated annotations — full annotation on UniProt →

Function. Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function.

Subcellular location. Mitochondrion.

Similarity. Belongs to the PTCD2 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8WV60-1	1	yes
Q8WV60-2	2
Q8WV60-3	3

RefSeq proteins (4): NP_001271332, NP_001271333, NP_001271334, NP_079030* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002885	PPR_rpt	Repeat
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR034629	PTCD2	Family
IPR034913	mS27/PTCD2	Family

Pfam: PF10037

UniProt features (9 total): splice variant 3, sequence conflict 3, chain 1, repeat 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WV60-F1	82.95	0.67

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 382

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): GOBP_CARDIAC_CHAMBER_DEVELOPMENT, GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_MUSCLE_TISSUE_DEVELOPMENT, GOBP_CARDIAC_CHAMBER_MORPHOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, GOBP_VENTRICULAR_CARDIAC_MUSCLE_TISSUE_DEVELOPMENT, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_HEART_MORPHOGENESIS, GOBP_CARDIAC_VENTRICLE_MORPHOGENESIS, GOBP_CARDIAC_MUSCLE_TISSUE_MORPHOGENESIS, GOBP_MUSCLE_ORGAN_MORPHOGENESIS, GOBP_CARDIAC_VENTRICLE_DEVELOPMENT

GO Biological Process (9): kidney development (GO:0001822), liver development (GO:0001889), mRNA processing (GO:0006397), mitochondrion organization (GO:0007005), regulation of gene expression (GO:0010468), regulation of mRNA processing (GO:0050684), muscle cell development (GO:0055001), ventricular cardiac muscle tissue morphogenesis (GO:0055010), heart development (GO:0007507)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
animal organ development	2
renal system development	1
gland development	1
hepaticobiliary system development	1
RNA processing	1
mRNA metabolic process	1
organelle organization	1
gene expression	1
regulation of macromolecule biosynthetic process	1
mRNA processing	1
regulation of mRNA metabolic process	1
muscle cell differentiation	1
cell development	1
cardiac ventricle morphogenesis	1
ventricular cardiac muscle tissue development	1
cardiac muscle tissue morphogenesis	1
circulatory system development	1
nucleic acid binding	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PTCD2	PTCD1	O75127	736
PTCD2	PTCD3	Q96EY7	681
PTCD2	PRORP	O15091	666
PTCD2	MRPS27	Q92552	595
PTCD2	FRMD8	Q9BZ67	570
PTCD2	LRPPRC	P42704	544
PTCD2	POLRMT	O00411	543
PTCD2	C1orf159	Q96HA4	527
PTCD2	ELAC2	Q9BQ52	491
PTCD2	DNHD1	Q96M86	490
PTCD2	TRMT10C	Q7L0Y3	488
PTCD2	ZNHIT2	Q9UHR6	466
PTCD2	GRSF1	Q12849	465
PTCD2	FRRS1L	Q9P0K9	460
PTCD2	ZNF106	Q9H2Y7	459

IntAct

44 interactions, top by confidence:

A	B	Type	Score
TSC22D4	TSC22D2	psi-mi:“MI:0914”(association)	0.640
MID1	PTCD2	psi-mi:“MI:0915”(physical association)	0.560
PTCD2	MID2	psi-mi:“MI:0915”(physical association)	0.560
TRIM32	PTCD2	psi-mi:“MI:0915”(physical association)	0.560
USP49	PTCD2	psi-mi:“MI:0915”(physical association)	0.560
VSIG4	TCAF2	psi-mi:“MI:0914”(association)	0.530
LRP1	NME4	psi-mi:“MI:0914”(association)	0.530
GTF2A1	INPPL1	psi-mi:“MI:0914”(association)	0.530
SALL2	GFPT2	psi-mi:“MI:0914”(association)	0.530
VTN	HAT1	psi-mi:“MI:0914”(association)	0.530
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
NTRK3	FAM171A2	psi-mi:“MI:0914”(association)	0.480
PTCD2	COP1	psi-mi:“MI:0915”(physical association)	0.400
PTCD2	NAA10	psi-mi:“MI:0915”(physical association)	0.400
HLA-E	RTL8C	psi-mi:“MI:0914”(association)	0.350
APP	ZNF724	psi-mi:“MI:0914”(association)	0.350
NTRK3	FAM171A2	psi-mi:“MI:0914”(association)	0.350
CLEC14A	PXK	psi-mi:“MI:0914”(association)	0.350
CDH8	ARVCF	psi-mi:“MI:0914”(association)	0.350
SLAMF7	APBB1	psi-mi:“MI:0914”(association)	0.350
VTN	HAT1	psi-mi:“MI:0914”(association)	0.350
SH2D3C	TMEM14DP	psi-mi:“MI:0914”(association)	0.350
RAMP2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
SLAMF7	HUS1	psi-mi:“MI:0914”(association)	0.350
CA6	PLXNA2	psi-mi:“MI:0914”(association)	0.350
TMEM154	VPS26A	psi-mi:“MI:0914”(association)	0.350

BioGRID (45): PTCD2 (Two-hybrid), PTCD2 (Two-hybrid), PTCD2 (Affinity Capture-RNA), PTCD2 (Affinity Capture-RNA), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS), PTCD2 (Affinity Capture-MS)

ESM2 similar proteins: A1A5P5, A1L2L5, A1Z9A8, B5DF07, O15091, P42704, Q07DV3, Q08CK1, Q0IHP3, Q14C51, Q14CX7, Q14CZ7, Q28C74, Q28DE0, Q2KI62, Q32LU7, Q32N55, Q32PI8, Q3SZ55, Q4R366, Q4R6I5, Q53R41, Q566X6, Q58CX2, Q5R503, Q5R8W8, Q5RFI6, Q5SGE0, Q5XIR8, Q5ZKK3, Q5ZLS8, Q68FN9, Q6AYP3, Q6DI86, Q6GQ66, Q6PB66, Q6QI44, Q7L8L6, Q7TMV3, Q7Z3E5

Diamond homologs: A1L2L5, Q3SZ55, Q566X6, Q5R503, Q8R3K3, Q8WV60

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

57 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2132 predictions. Top by Δscore:

Variant	Effect	Δscore
5:72322162:T:TA	acceptor_gain	1.0000
5:72322167:TTTA:T	acceptor_loss	1.0000
5:72322170:A:AG	acceptor_gain	1.0000
5:72322171:G:GG	acceptor_gain	1.0000
5:72322171:GCT:G	acceptor_gain	1.0000
5:72322171:GCTA:G	acceptor_gain	1.0000
5:72322171:GCTAA:G	acceptor_gain	1.0000
5:72322260:TAAAG:T	donor_loss	1.0000
5:72322261:AAAGG:A	donor_loss	1.0000
5:72322262:AAG:A	donor_loss	1.0000
5:72322263:AGGT:A	donor_loss	1.0000
5:72322265:G:GA	donor_loss	1.0000
5:72322266:T:G	donor_loss	1.0000
5:72335882:ACTGG:A	donor_loss	1.0000
5:72335883:CTGGT:C	donor_loss	1.0000
5:72335886:G:GC	donor_loss	1.0000
5:72335886:G:GG	donor_gain	1.0000
5:72335887:T:A	donor_loss	1.0000
5:72338620:A:AG	acceptor_gain	1.0000
5:72338621:G:GG	acceptor_gain	1.0000
5:72338621:GAATA:G	acceptor_gain	1.0000
5:72355641:GCT:G	donor_gain	1.0000
5:72320507:G:GT	donor_gain	0.9900
5:72321378:T:G	donor_gain	0.9900
5:72322171:GC:G	acceptor_gain	0.9900
5:72335788:T:A	acceptor_gain	0.9900
5:72335788:TGGCA:T	acceptor_loss	0.9900
5:72335789:GGCA:G	acceptor_loss	0.9900
5:72335790:GCA:G	acceptor_loss	0.9900
5:72335791:CA:C	acceptor_loss	0.9900

AlphaMissense

2554 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:72322216:T:C	F58L	0.984
5:72322218:T:A	F58L	0.984
5:72322218:T:G	F58L	0.984
5:72331325:T:C	C140R	0.977
5:72335051:T:C	F168L	0.971
5:72335053:C:A	F168L	0.971
5:72335053:C:G	F168L	0.971
5:72335869:C:A	A208E	0.971
5:72326675:T:C	L95S	0.969
5:72331321:G:C	R138S	0.969
5:72331321:G:T	R138S	0.969
5:72335797:C:A	A184D	0.965
5:72322217:T:C	F58S	0.964
5:72331320:G:C	R138T	0.964
5:72335874:T:C	C210R	0.962
5:72338725:C:A	A248D	0.958
5:72335818:T:C	M191T	0.957
5:72338728:T:C	L249P	0.957
5:72331301:T:C	F132L	0.955
5:72331303:T:A	F132L	0.955
5:72331303:T:G	F132L	0.955
5:72335884:T:C	L213P	0.955
5:72335868:G:C	A208P	0.954
5:72335863:C:A	A206D	0.953
5:72335033:T:C	F162L	0.952
5:72335035:C:A	F162L	0.952
5:72335035:C:G	F162L	0.952
5:72338724:G:C	A248P	0.952
5:72335076:T:C	F176S	0.949
5:72326723:C:A	A111D	0.947

dbSNP variants (sampled 300 via entrez): RS1000060579 (5:72323701 G>A,C), RS1000137149 (5:72334264 C>T), RS1000191777 (5:72330440 T>A,C), RS1000214839 (5:72324914 T>G), RS1000264410 (5:72337152 C>A,G), RS1000417856 (5:72365444 C>A,G,T), RS1000418106 (5:72318399 T>C), RS1000469373 (5:72351271 T>C), RS1000475669 (5:72328432 C>G,T), RS1000479746 (5:72343754 A>C,G), RS1000538163 (5:72323330 T>C), RS1000677624 (5:72344521 G>T), RS1000712976 (5:72335381 G>A,T), RS1000759692 (5:72358504 C>A,T), RS1000780962 (5:72336819 A>G)

Disease associations

OMIM: gene MIM:615484 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST005580_261	Intraocular pressure	2.000000e-10
GCST005580_84	Intraocular pressure	3.000000e-11
GCST006394_42	Intraocular pressure	7.000000e-09
GCST006412_47	Intraocular pressure	8.000000e-10
GCST007096_24	Pulse pressure	4.000000e-09
GCST007995_22	Asthma (childhood onset)	5.000000e-08
GCST009725_82	Intraocular pressure	3.000000e-07
GCST009726_10	Glaucoma	6.000000e-06
GCST010002_30	Refractive error	1.000000e-12
GCST010042_134	Asthma	3.000000e-08
GCST010241_290	Apolipoprotein A1 levels	6.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0005763	pulse pressure measurement
EFO:0004614	apolipoprotein A 1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
1-nitropyrene	increases expression	1
pentanal	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	increases expression	1
Arsenic	decreases expression, affects cotreatment, increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Silicon Dioxide	decreases expression	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Vanadates	increases expression	1
Oxyquinoline	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.