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

Gene Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	10667
Gene name Gene Name - the full gene name approved by the HGNC.	Phenylalanyl-tRNA synthetase 2, mitochondrial
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	FARS2
Synonyms (NCBI Gene) Gene synonyms aliases	COXPD14, FARS1, HSPC320, PheRS, SPG77, mtPheRS
Chromosome Chromosome number	6
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	6p25.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein that transfers phenylalanine to its cognate tRNA. This protein localizes to the mitochondrion and plays a role in mitochondrial protein translation. Mutations in this gene can cause combined oxidative phosphorylation deficiency

Show/Hide all(32)

SNP ID	Visualize variation	Clinical significance	Consequence
rs142073519	A>G	Likely-pathogenic, uncertain-significance	Non coding transcript variant, downstream transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs145555213	G>A,T	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs146356199	A>G,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs146988468	C>A,T	Likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs148620369	C>T	Uncertain-significance, pathogenic	Genic downstream transcript variant, coding sequence variant, stop gained, non coding transcript variant
rs148921184	G>A	Uncertain-significance, likely-pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs202060864	C>T	Likely-pathogenic, conflicting-interpretations-of-pathogenicity	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, missense variant
rs202183509	G>A,T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant
rs372054960	C>T	Uncertain-significance, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs397514610	A>G	Pathogenic, likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs397514611	T>C	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, downstream transcript variant, missense variant, non coding transcript variant
rs397514612	A>T	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs554931092	G>A	Likely-pathogenic, uncertain-significance	Intron variant, coding sequence variant, non coding transcript variant, missense variant
rs746746116	G>A,C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant, genic downstream transcript variant
rs749588235	C>T	Likely-pathogenic	Intron variant, non coding transcript variant, coding sequence variant, missense variant
rs751459058	C>T	Pathogenic, conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant, genic downstream transcript variant
rs761097220	A>-	Likely-pathogenic, uncertain-significance	Intron variant, coding sequence variant, non coding transcript variant, frameshift variant
rs761709212	C>G	Pathogenic	Stop gained, intron variant, coding sequence variant, non coding transcript variant
rs764427452	G>A,T	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant, downstream transcript variant
rs770035560	C>G	Likely-pathogenic	Intron variant, coding sequence variant, missense variant, non coding transcript variant
rs775690041	C>T	Likely-pathogenic	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs1057523346	C>T	Likely-pathogenic	Stop gained, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs1229314240	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, stop gained
rs1298860043	G>A,T	Likely-pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1322974029	TTAGA>-	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs1407198979	T>A,C,G	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant, genic downstream transcript variant
rs1429774361	C>-	Pathogenic	Intron variant, frameshift variant, non coding transcript variant, coding sequence variant
rs1554169280	C>G	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant, intron variant
rs1554169353	C>G	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant, intron variant
rs1561990337	A>G	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant, intron variant
rs1561990390	A>C	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, non coding transcript variant, intron variant
rs1561990552	T>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant, intron variant

Show/Hide all(26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IDA	10329163
GO:0000049	Function	TRNA binding	IEA
GO:0000166	Function	Nucleotide binding	IEA
GO:0004812	Function	Aminoacyl-tRNA ligase activity	IEA
GO:0004826	Function	Phenylalanine-tRNA ligase activity	IBA
GO:0004826	Function	Phenylalanine-tRNA ligase activity	IDA	10329163
GO:0004826	Function	Phenylalanine-tRNA ligase activity	IEA
GO:0004826	Function	Phenylalanine-tRNA ligase activity	TAS
GO:0005515	Function	Protein binding	IPI	25416956, 28514442, 31515488, 32296183, 33961781
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	ISS
GO:0005759	Component	Mitochondrial matrix	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006412	Process	Translation	IEA
GO:0006418	Process	TRNA aminoacylation for protein translation	TAS
GO:0006432	Process	Phenylalanyl-tRNA aminoacylation	IBA
GO:0006432	Process	Phenylalanyl-tRNA aminoacylation	IDA	10329163
GO:0006432	Process	Phenylalanyl-tRNA aminoacylation	IEA
GO:0008033	Process	TRNA processing	IDA	10329163
GO:0016874	Function	Ligase activity	IEA
GO:0043039	Process	TRNA aminoacylation	IEA

MIM	HGNC	e!Ensembl
611592	21062	ENSG00000145982

Protein

UniProt ID

O95363

Protein name

Phenylalanine--tRNA ligase, mitochondrial (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase) (PheRS)

Protein function

Is responsible for the charging of tRNA(Phe) with phenylalanine in mitochondrial translation. To a lesser extent, also catalyzes direct attachment of m-Tyr (an oxidized version of Phe) to tRNA(Phe), thereby opening the way for delivery of the mi

PDB

3CMQ , 3HFV , 3TEG , 3TUP , 5MGH , 5MGU , 5MGV , 5MGW , 8P8X

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01409	tRNA-synt_2d	70 → 210	tRNA synthetases class II core domain (F)	Domain
PF01409	tRNA-synt_2d	219 → 343	tRNA synthetases class II core domain (F)	Domain
PF03147	FDX-ACB	358 → 450	Ferredoxin-fold anticodon binding domain	Domain

Sequence

MVGSALRRGAHAYVYLVSKASHISRGHQHQAWGSRPPAAECATQRAPGSVVELLGKSYPQ
DDHSNLTRKVLTRVGRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVV
TTWQNFDSLLIPADHPSRKKGDNYYLNRTHMLRAHTSAHQWDLLHAGLDAFLVVGDVYRR
DQIDSQHYPIFHQLEAVRLFSKHELFAGIKDGESLQLFEQSSRSAHKQETHTMEAVKLVE
FDLKQTLTRLMAHLFGDELEIRWVDCYFPFTHPSFEMEINFHGEWLEVLGCGVMEQQLVN
SAGAQDRIGWAFGLGLERLAMILYDIPDIRLFWCEDERFLKQFCVSNINQKVKFQPLSKY
PAVINDISFWLPSENYAENDFYDLVRTIGGDLVEKVDLIDKFVHPKTHKTSHCYRITYRH
MERTLSQREVRHIHQALQEAAVQLLGVEGRF

Sequence length

451

Interactions

View interactions

	KEGG		Reactome
	Aminoacyl-tRNA biosynthesis		Mitochondrial tRNA aminoacylation

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Combined Oxidative Phosphorylation Deficiency	combined oxidative phosphorylation defect type 14	rs1561990552, rs1554169353, rs148620369, rs1298860043, rs751459058, rs1554169280, rs746746116, rs1407198979, rs1229314240, rs1322974029, rs1429774361, rs775690041, rs761709212, rs764427452, rs1554116357 View all (8 more)	N/A
Hereditary spastic paraplegia	Hereditary spastic paraplegia 77	rs751459058, rs775690041, rs145555213, rs761097220, rs202183509	N/A
leigh syndrome	Leigh syndrome	rs761097220	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Metabolic Diseases	metabolic disease	N/A	N/A	GenCC
Neuroblastoma	Neuroblastoma	N/A	N/A	GWAS

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Brain Diseases	Associate	33168986, 36155627
Cytochrome c Oxidase Deficiency	Associate	24161539
Developmental Disabilities	Associate	36155627
Diffuse Cerebral Sclerosis of Schilder	Associate	28419689, 31241862
Disease	Associate	27095821, 33168986
Drug Resistant Epilepsy	Associate	27095821
Encephalopathy Spastic Tetraparesis and Hypogonadism	Associate	33168986
Epilepsies Myoclonic	Associate	33168986
Epilepsy	Associate	24161539, 29126765, 33168986
Epilepsy Benign Neonatal	Associate	24161539
Immunologic Deficiency Syndromes	Associate	29126765
Liver Failure	Associate	36155627
MERRF Syndrome	Associate	32115907
Migraine Disorders	Associate	35546551
Mitochondrial Diseases	Associate	24161539, 28419689, 29126765
Mitochondrial encephalopathy	Associate	33168986
Muscle Hypotonia	Associate	33168986, 36155627
Muscle Neoplasms	Associate	32115907
Myoclonic Epilepsies Progressive	Associate	27095821
Neurologic Manifestations	Associate	24161539, 32115907
Paraplegia	Associate	28419689, 29126765, 31241862, 33168986

FARS2 (phenylalanyl-tRNA synthetase 2, mitochondrial)