Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	29920
Gene name	Pyrroline-5-carboxylate reductase 2
Gene symbol	PYCR2
Synonyms (NCBI Gene)	HLD10P5CR2
Chromosome	1
Chromosome location	1q42.12
Summary	This gene belongs to the pyrroline-5-carboxylate reductase family. The encoded mitochondrial protein catalyzes the conversion of pyrroline-5-carboxylate to proline, which is the last step in proline biosynthesis. Alternatively spliced transcript variants

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs876657403	G>A	Pathogenic	Missense variant, coding sequence variant
rs886037931	G>A	Pathogenic	Coding sequence variant, stop gained
rs886037932	A>G	Pathogenic	Coding sequence variant, missense variant
rs886037933	A>C	Pathogenic	Coding sequence variant, missense variant
rs886043378	AG>-,AGAG	Pathogenic-likely-pathogenic	Frameshift variant, coding sequence variant

109

Show/Hide all (109)

miRTarBase ID	miRNA	Experiments	Reference
MIRT028646	hsa-miR-30a-5p	Proteomics	18668040
MIRT040656	hsa-miR-92b-3p	CLASH	23622248
MIRT1279312	hsa-miR-3130-5p	CLIP-seq
MIRT1279313	hsa-miR-4424	CLIP-seq
MIRT1279314	hsa-miR-4482	CLIP-seq
MIRT1279315	hsa-miR-451b	CLIP-seq
MIRT1279316	hsa-miR-4694-3p	CLIP-seq
MIRT1279317	hsa-miR-486-5p	CLIP-seq
MIRT1279318	hsa-miR-500a	CLIP-seq
MIRT1279319	hsa-miR-522	CLIP-seq
MIRT1279320	hsa-miR-758	CLIP-seq
MIRT2082315	hsa-miR-1178	CLIP-seq
MIRT2082316	hsa-miR-1207-3p	CLIP-seq
MIRT2082317	hsa-miR-1231	CLIP-seq
MIRT2082318	hsa-miR-1273e	CLIP-seq
MIRT2082319	hsa-miR-141	CLIP-seq
MIRT2082320	hsa-miR-149	CLIP-seq
MIRT2082321	hsa-miR-200a	CLIP-seq
MIRT2082322	hsa-miR-2115	CLIP-seq
MIRT2082323	hsa-miR-296-3p	CLIP-seq
MIRT2082324	hsa-miR-3064-5p	CLIP-seq
MIRT2082325	hsa-miR-3124-3p	CLIP-seq
MIRT2082326	hsa-miR-3125	CLIP-seq
MIRT2082327	hsa-miR-3127-3p	CLIP-seq
MIRT1279312	hsa-miR-3130-5p	CLIP-seq
MIRT2082328	hsa-miR-3150b-3p	CLIP-seq
MIRT2082329	hsa-miR-3160-5p	CLIP-seq
MIRT2082330	hsa-miR-3184	CLIP-seq
MIRT2082331	hsa-miR-338-3p	CLIP-seq
MIRT2082332	hsa-miR-382	CLIP-seq
MIRT2082333	hsa-miR-3916	CLIP-seq
MIRT2082334	hsa-miR-3925-3p	CLIP-seq
MIRT2082335	hsa-miR-3944-3p	CLIP-seq
MIRT2082336	hsa-miR-423-5p	CLIP-seq
MIRT2082337	hsa-miR-4279	CLIP-seq
MIRT2082338	hsa-miR-4300	CLIP-seq
MIRT1279313	hsa-miR-4424	CLIP-seq
MIRT2082339	hsa-miR-4457	CLIP-seq
MIRT1279314	hsa-miR-4482	CLIP-seq
MIRT1279315	hsa-miR-451b	CLIP-seq
MIRT2082340	hsa-miR-4530	CLIP-seq
MIRT2082341	hsa-miR-4688	CLIP-seq
MIRT2082342	hsa-miR-4689	CLIP-seq
MIRT1279316	hsa-miR-4694-3p	CLIP-seq
MIRT2082343	hsa-miR-4711-3p	CLIP-seq
MIRT2082344	hsa-miR-4779	CLIP-seq
MIRT2082345	hsa-miR-4781-5p	CLIP-seq
MIRT2082346	hsa-miR-4784	CLIP-seq
MIRT2082347	hsa-miR-4794	CLIP-seq
MIRT2082348	hsa-miR-502-5p	CLIP-seq
MIRT2082349	hsa-miR-508-5p	CLIP-seq
MIRT2082350	hsa-miR-513b	CLIP-seq
MIRT1279319	hsa-miR-522	CLIP-seq
MIRT2082351	hsa-miR-541	CLIP-seq
MIRT2082352	hsa-miR-592	CLIP-seq
MIRT2082353	hsa-miR-599	CLIP-seq
MIRT2082354	hsa-miR-654-5p	CLIP-seq
MIRT2082355	hsa-miR-744	CLIP-seq
MIRT2082356	hsa-miR-891b	CLIP-seq
MIRT2082357	hsa-miR-920	CLIP-seq
MIRT2082318	hsa-miR-1273e	CLIP-seq
MIRT2307954	hsa-miR-1302	CLIP-seq
MIRT2082326	hsa-miR-3125	CLIP-seq
MIRT1279312	hsa-miR-3130-5p	CLIP-seq
MIRT2307955	hsa-miR-3173-3p	CLIP-seq
MIRT2082333	hsa-miR-3916	CLIP-seq
MIRT2307956	hsa-miR-4298	CLIP-seq
MIRT2307957	hsa-miR-4428	CLIP-seq
MIRT2307958	hsa-miR-4477b	CLIP-seq
MIRT1279314	hsa-miR-4482	CLIP-seq
MIRT2307959	hsa-miR-4527	CLIP-seq
MIRT2307960	hsa-miR-4539	CLIP-seq
MIRT2307961	hsa-miR-4768-3p	CLIP-seq
MIRT1279317	hsa-miR-486-5p	CLIP-seq
MIRT1279318	hsa-miR-500a	CLIP-seq
MIRT1279312	hsa-miR-3130-5p	CLIP-seq
MIRT1279314	hsa-miR-4482	CLIP-seq
MIRT1279317	hsa-miR-486-5p	CLIP-seq
MIRT1279318	hsa-miR-500a	CLIP-seq
MIRT2082317	hsa-miR-1231	CLIP-seq
MIRT2082320	hsa-miR-149	CLIP-seq
MIRT2082322	hsa-miR-2115	CLIP-seq
MIRT2082323	hsa-miR-296-3p	CLIP-seq
MIRT2082324	hsa-miR-3064-5p	CLIP-seq
MIRT2082331	hsa-miR-338-3p	CLIP-seq
MIRT2082334	hsa-miR-3925-3p	CLIP-seq
MIRT2605203	hsa-miR-4323	CLIP-seq
MIRT2605204	hsa-miR-4468	CLIP-seq
MIRT2082340	hsa-miR-4530	CLIP-seq
MIRT2082343	hsa-miR-4711-3p	CLIP-seq
MIRT2082347	hsa-miR-4794	CLIP-seq
MIRT2605205	hsa-miR-503	CLIP-seq
MIRT2082349	hsa-miR-508-5p	CLIP-seq
MIRT2082352	hsa-miR-592	CLIP-seq
MIRT2082353	hsa-miR-599	CLIP-seq
MIRT2082317	hsa-miR-1231	CLIP-seq
MIRT2082320	hsa-miR-149	CLIP-seq
MIRT2082322	hsa-miR-2115	CLIP-seq
MIRT2082323	hsa-miR-296-3p	CLIP-seq
MIRT2082324	hsa-miR-3064-5p	CLIP-seq
MIRT2082334	hsa-miR-3925-3p	CLIP-seq
MIRT2605203	hsa-miR-4323	CLIP-seq
MIRT2605204	hsa-miR-4468	CLIP-seq
MIRT2082343	hsa-miR-4711-3p	CLIP-seq
MIRT2082347	hsa-miR-4794	CLIP-seq
MIRT2605205	hsa-miR-503	CLIP-seq
MIRT2082349	hsa-miR-508-5p	CLIP-seq
MIRT2082352	hsa-miR-592	CLIP-seq
MIRT2082353	hsa-miR-599	CLIP-seq

Show/Hide all (17)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004735	Function	Pyrroline-5-carboxylate reductase activity	IBA
GO:0004735	Function	Pyrroline-5-carboxylate reductase activity	IDA	23024808
GO:0004735	Function	Pyrroline-5-carboxylate reductase activity	IEA
GO:0005515	Function	Protein binding	IPI	24930674
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	23024808, 25865492
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005829	Component	Cytosol	TAS
GO:0008652	Process	Amino acid biosynthetic process	IEA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0034599	Process	Cellular response to oxidative stress	IEA
GO:0034599	Process	Cellular response to oxidative stress	IMP	25865492
GO:0055129	Process	L-proline biosynthetic process	IBA
GO:0055129	Process	L-proline biosynthetic process	IDA	23024808
GO:0055129	Process	L-proline biosynthetic process	IEA

MIM	HGNC	e!Ensembl
616406	30262	ENSG00000143811

Q96C36

Protein name

Pyrroline-5-carboxylate reductase 2 (P5C reductase 2) (P5CR 2) (EC 1.5.1.2)

Protein function

Oxidoreductase that catalyzes the last step in proline biosynthesis, which corresponds to the reduction of pyrroline-5-carboxylate to L-proline using NAD(P)H (PubMed:23024808, PubMed:2722838, PubMed:6894153). At physiologic concentrations, has h

PDB

6LHM

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03807	F420_oxidored	2 → 98	NADP oxidoreductase coenzyme F420-dependent	Family
PF14748	P5CR_dimer	164 → 268	Pyrroline-5-carboxylate reductase dimerisation	Domain

Tissue specificity

TISSUE SPECIFICITY: Detected in erythrocytes (at protein level) (PubMed:2722838, PubMed:6894153). Expressed in fetal brain (PubMed:25865492). {ECO:0000269|PubMed:25865492, ECO:0000269|PubMed:2722838, ECO:0000269|PubMed:6894153}.

Sequence

MSVGFIGAGQLAYALARGFTAAGILSAHKIIASSPEMNLPTVSALRKMGVNLTRSNKETV
KHSDVLFLAVKPHIIPFILDEIGADVQARHIVVSCAAGVTISSVEKKLMAFQPAPKVIRC
MTNTPVVVQEGATVYATGTHALVEDGQLLEQLMSSVGFCTEVEEDLIDAVTGLSGSGPAY
AFMALDALADGGVKMGLPRRLAIQLGAQALLGAAKMLLDSEQHPCQLKDNVCSPGGATIH
ALHFLESGGFRSLLINAVEASCIRTRELQSMADQEKISPAALKKTLLDRVKLESPTVSTL
TPSSPGKLLTRSLALGGKKD

Sequence length

320

Interactions

View interactions

	KEGG		Reactome
	Arginine and proline metabolism Metabolic pathways Biosynthesis of amino acids		Glutamate and glutamine metabolism

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hypomyelinating leukodystrophy 10	Likely pathogenic; Pathogenic	rs201784173, rs2102672664, rs2102672881, rs2102672892, rs372781135, rs876657403, rs35240460, rs886037931, rs886037932, rs886037933, rs886043378, rs745824721, rs149587849, rs1553500497, rs1473859981 View all (4 more)	RCV001814814 RCV001784890 RCV001783651 RCV002503396 RCV000173021 View all (14 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leukodystrophy	Pathogenic	rs886037931	RCV004798819	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
AUTOSOMAL RECESSIVE PRIMARY MICROCEPHALY	—	Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, BASAL CELL	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, 10	—	CTD, HPO CTD, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PYCR2-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (39)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arachnodactyly	Arachnodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Autosomal Recessive Primary Microcephaly	Microcephaly	ORPHANET_DG	27860360		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive primary microcephaly	Microcephaly	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	38101533	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	37508547	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	36624948	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	34512817, 38101533	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	37508547	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Demyelinating Diseases	Demyelinating diseases	Pubtator	25865492, 33771508	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Depression Postpartum	Major depressive disorder	Pubtator	25865492, 33771508	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperkinesis	Hyperkinesia	Pubtator	27130255	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	27860360		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukodystrophy	Leukodystrophy	BEFREE	27860360		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Leukodystrophy	Leukodystrophy	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
LEUKODYSTROPHY, HYPOMYELINATING, 10	Leukodystrophy	CLINVAR_DG	25865492, 27860360		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, 10	Leukodystrophy	UNIPROT_DG	25865492		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, 10	Leukodystrophy	ORPHANET_DG	27130255		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, 10	Leukodystrophy	GENOMICS_ENGLAND_DG	27860360		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, 10	Leukodystrophy	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Liver carcinoma	Liver carcinoma	BEFREE	31585088		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	26634742		★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	26634742	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	25865492, 27130255, 27860360		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	Pubtator	25865492, 27130255, 33771508	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mitochondrial Diseases	Mitochondrial disease	Pubtator	27130255	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuronal heterotopia	Neuronal Heterotopia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Psychomotor Disorders	Psychiatric disorders	Pubtator	27130255	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
PYCR2-related microcephaly-progressive leukoencephalopathy	Microcephaly-Progressive Leukoencephalopathy	Orphanet			★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	30559182		★★★★★ ★☆☆☆☆ Found in Text Mining only
Unilateral agenesis of kidney	Renal aplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Vesico-Ureteral Reflux	Vesicoureteral Reflux	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

PYCR2 (pyrroline-5-carboxylate reductase 2)