FARSB (phenylalanyl-tRNA synthetase subunit beta)

Gene

• Entrez ID: 10056
• Gene name: Phenylalanyl-tRNA synthetase subunit beta
• Gene symbol: FARSB
• Synonyms (NCBI Gene): FARSLB, FRSB, HSPC173, NEDBLLA, PheHB, PheRS, RILDBC, RILDBC1, RJBS
• Chromosome: 2
• Chromosome location: 2q36.1
• Summary: This gene encodes a highly conserved enzyme that belongs to the aminoacyl-tRNA synthetase class IIc subfamily. This enzyme comprises the regulatory beta subunits that form a tetramer with two catalytic alpha subunits. In the presence of ATP, this tetramer

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs753710639	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs767956337	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs773579570	C>T	Likely-pathogenic, pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs777071414	C>G,T	Pathogenic	Splice donor variant
rs1396171148	T>G	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1419129874	A>G	Pathogenic	5 prime UTR variant, non coding transcript variant, missense variant, coding sequence variant
rs1466642025	A>G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs1553549333	G>TT	Pathogenic, likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553553086	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553554543	T>C	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT048577	hsa-miR-100-5p	CLASH	23622248
MIRT041199	hsa-miR-193b-3p	CLASH	23622248
MIRT037617	hsa-miR-744-5p	CLASH	23622248
MIRT518613	hsa-miR-590-3p	PAR-CLIP	23446348
MIRT518612	hsa-miR-3681-5p	PAR-CLIP	23446348
MIRT518611	hsa-miR-6849-5p	PAR-CLIP	23446348
MIRT518610	hsa-miR-4735-5p	PAR-CLIP	23446348
MIRT518608	hsa-miR-1273f	PAR-CLIP	23446348
MIRT518609	hsa-miR-4683	PAR-CLIP	23446348
MIRT518607	hsa-miR-4775	PAR-CLIP	23446348
MIRT518606	hsa-miR-4727-3p	PAR-CLIP	23446348
MIRT518605	hsa-miR-1270	PAR-CLIP	23446348
MIRT518604	hsa-miR-620	PAR-CLIP	23446348
MIRT518603	hsa-miR-3591-5p	PAR-CLIP	23446348
MIRT518602	hsa-miR-6083	PAR-CLIP	23446348
MIRT518613	hsa-miR-590-3p	PAR-CLIP	23446348
MIRT518612	hsa-miR-3681-5p	PAR-CLIP	23446348
MIRT518611	hsa-miR-6849-5p	PAR-CLIP	23446348
MIRT518610	hsa-miR-4735-5p	PAR-CLIP	23446348
MIRT518608	hsa-miR-1273f	PAR-CLIP	23446348
MIRT518609	hsa-miR-4683	PAR-CLIP	23446348
MIRT518607	hsa-miR-4775	PAR-CLIP	23446348
MIRT518606	hsa-miR-4727-3p	PAR-CLIP	23446348
MIRT518605	hsa-miR-1270	PAR-CLIP	23446348
MIRT518604	hsa-miR-620	PAR-CLIP	23446348
MIRT518603	hsa-miR-3591-5p	PAR-CLIP	23446348
MIRT518602	hsa-miR-6083	PAR-CLIP	23446348
MIRT989468	hsa-miR-1228	CLIP-seq
MIRT989469	hsa-miR-140-3p	CLIP-seq
MIRT989470	hsa-miR-3123	CLIP-seq
MIRT989471	hsa-miR-450b-3p	CLIP-seq
MIRT989472	hsa-miR-4646-5p	CLIP-seq
MIRT989473	hsa-miR-4713-3p	CLIP-seq
MIRT989474	hsa-miR-4747-5p	CLIP-seq
MIRT989475	hsa-miR-638	CLIP-seq
MIRT989476	hsa-miR-769-3p	CLIP-seq
MIRT1993268	hsa-miR-1197	CLIP-seq
MIRT1993269	hsa-miR-183	CLIP-seq
MIRT989470	hsa-miR-3123	CLIP-seq
MIRT1993270	hsa-miR-320e	CLIP-seq
MIRT1993271	hsa-miR-339-5p	CLIP-seq
MIRT1993272	hsa-miR-4477b	CLIP-seq
MIRT989472	hsa-miR-4646-5p	CLIP-seq
MIRT989474	hsa-miR-4747-5p	CLIP-seq
MIRT1993273	hsa-miR-4774-5p	CLIP-seq
MIRT1993274	hsa-miR-765	CLIP-seq
MIRT2227112	hsa-miR-1301	CLIP-seq
MIRT2227113	hsa-miR-377	CLIP-seq
MIRT2227114	hsa-miR-4660	CLIP-seq
MIRT2227115	hsa-miR-5047	CLIP-seq
MIRT1993274	hsa-miR-765	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000287	Function	Magnesium ion binding	IEA
GO:0000287	Function	Magnesium ion binding	ISS
GO:0003723	Function	RNA binding	IEA
GO:0004812	Function	Aminoacyl-tRNA ligase activity	IEA
GO:0004826	Function	Phenylalanine-tRNA ligase activity	IDA	20223217
GO:0004826	Function	Phenylalanine-tRNA ligase activity	IEA
GO:0004826	Function	Phenylalanine-tRNA ligase activity	TAS	10049785
GO:0005515	Function	Protein binding	IPI	20223217, 28514442, 32296183, 32814053, 33961781
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	20223217
GO:0005737	Component	Cytoplasm	TAS	10049785
GO:0005829	Component	Cytosol	TAS
GO:0006412	Process	Translation	IEA
GO:0006412	Process	Translation	TAS	10049785
GO:0006432	Process	Phenylalanyl-tRNA aminoacylation	IBA
GO:0006432	Process	Phenylalanyl-tRNA aminoacylation	IDA	20223217
GO:0006432	Process	Phenylalanyl-tRNA aminoacylation	IEA
GO:0009328	Component	Phenylalanine-tRNA ligase complex	IBA
GO:0009328	Component	Phenylalanine-tRNA ligase complex	IDA	20223217
GO:0009328	Component	Phenylalanine-tRNA ligase complex	IPI	20223217
GO:0016020	Component	Membrane	HDA	19946888
GO:0016874	Function	Ligase activity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051290	Process	Protein heterotetramerization	IDA	20223217

Other IDs

• MIM: 609690
• HGNC: 17800
• e!Ensembl: ENSG00000116120

Protein

• UniProt ID: Q9NSD9
• Protein name: Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS)
• PDB: 3L4G
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF18262	PhetRS_B1	1 → 90	Phe-tRNA synthetase beta subunit B1 domain	Domain
  PF03483	B3_4	117 → 279	B3/4 domain	Domain
  PF03484	B5	308 → 374	tRNA synthetase B5 domain	Domain
  PF17759	tRNA_synthFbeta	377 → 585	Phenylalanyl tRNA synthetase beta chain CLM domain	Domain

• Sequence:

  MPTVSVKRDLLFQALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNVKAAGASDV
  VLYKIDVPANRYDLLCLEGLVRGLQVFKERIKAPVYKRVMPDGKIQKLIITEETAKIRPF
  AVAAVLRNIKFTKDRYDSFIELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKRPSD
  IKFKPLNKTKEYTACELMNIYKTDNHLKHYLHIIENKPLYPVIYDSNGVVLSMPPIINGD
  HSRITVNTRNIFIECTGTDFTKAKIVLDIIVTMFSEYCENQFTVEAAEVVFPNGKSHTFP
  ELAYRKEMVRADLINKKVGIRETPENLAKLLTRMYLKSEVIGDGNQIEIEIPPTRADIIH
  ACDIVEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRHDMAAAGFTEALTFALCSQ
  EDIADKLGVDISATKAVHISNPKTAEFQVARTTLLPGLLKTIAANRKMPLPLKLFEISDI
  VIKDSNTDVGAKNYRHLCAVYYNKNPGFEIIHGLLDRIMQLLDVPPGEDKGGYVIKASEG
  PAFFPGRCAEIFARGQSVGKLGVLHPDVITKFELTMPCSSLEINVGPFL

• Sequence length: 589

Pathways

KEGG:

Aminoacyl-tRNA biosynthesis

Reactome:

Cytosolic tRNA aminoacylation

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cerebral calcification	Pathogenic	rs1396171148, rs1553554543, rs1553553086, rs1466642025, rs1419129874	RCV000656663 RCV000656689 RCV000656702 RCV000656728 RCV000656729	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cirrhosis of liver	Pathogenic	rs1396171148, rs1553554543, rs1553553086, rs1466642025, rs1419129874	RCV000656663 RCV000656689 RCV000656702 RCV000656728 RCV000656729	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Interstitial pneumonitis	Pathogenic	rs1396171148, rs1553554543, rs1553553086, rs1466642025, rs1419129874	RCV000656663 RCV000656689 RCV000656702 RCV000656728 RCV000656729	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Rajab interstitial lung disease with brain calcifications	Pathogenic; Likely pathogenic	rs1553549333, rs773579570, rs777071414, rs1396171148, rs1553553086, rs1466642025, rs767956337	RCV000656392 RCV000754847 RCV000754845 RCV000754849 RCV000754848 RCV000754850 RCV000754846	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Rajab interstitial lung disease with brain calcifications 1	Pathogenic; Likely pathogenic	rs2106209945, rs2106230623, rs777071414, rs767956337	RCV002249980 RCV002249981 RCV002499132 RCV004595857	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe early-onset pulmonary alveolar proteinosis due to MARS deficiency	Pathogenic	rs1553549333	RCV000677233	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Vascular dilatation	Pathogenic	rs1396171148, rs1553554543, rs1553553086, rs1466642025, rs1419129874	RCV000656663 RCV000656689 RCV000656702 RCV000656728 RCV000656729	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BRAIN CALCIFICATION RAJAB TYPE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FARSB-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTERSTITIAL LUNG DISEASE-BRAIN CALCIFICATION SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER CIRRHOSIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Brain calcification Rajab type	Rajab interstitial lung disease with brain calcifications	UNIPROT_DG	29573043, 29979980, 30014610		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain calcification Rajab type	Rajab interstitial lung disease with brain calcifications	GENOMICS_ENGLAND_DG	30014610		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain calcification Rajab type	Rajab interstitial lung disease with brain calcifications	ORPHANET_DG	30014610		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain calcification Rajab type	Rajab interstitial lung disease with brain calcifications	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain calcification Rajab type	Rajab interstitial lung disease with brain calcifications	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain calcification, Rajab type	Brain Calcification	Orphanet			★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	35132614	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	40497472	Associate	★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	37074800, 38069034	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	40621461	Associate	★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholestasis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	35132614	Associate	★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	HPO_DG			★☆☆☆☆ Found in Text Mining only
Gastroesophageal reflux disease	Gastroesophageal Reflux Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoalbuminemia	Hypoalbuminemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	30014610		★☆☆☆☆ Found in Text Mining only
INTERSTITIAL LUNG AND LIVER DISEASE	Interstitial Lung And Liver Disease	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis	Liver Cirrhosis	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung Diseases Interstitial	Lung disease	Pubtator	35132614	Associate	★☆☆☆☆ Found in Text Mining only
Lung Diseases, Interstitial	Lung Diseases	BEFREE	30014610, 31355908		★☆☆☆☆ Found in Text Mining only
Lung Diseases, Interstitial	Lung Diseases	GENOMICS_ENGLAND_DG	30014610		★☆☆☆☆ Found in Text Mining only
Lung Diseases, Interstitial	Lung Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	GENOMICS_ENGLAND_DG	30014610		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pancytopenia	Pancytopenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Portal Hypertension	Portal Hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary Alveolar Proteinosis	Alveolar proteinosis	BEFREE	31002528		★☆☆☆☆ Found in Text Mining only
Rickets	Rickets	HPO_DG			★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	HPO_DG			★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	34159625, 37074800	Stimulate	★☆☆☆☆ Found in Text Mining only
Vesico-Ureteral Reflux	Vesicoureteral Reflux	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only