FARSB

phenylalanyl-tRNA synthetase subunit beta, the group of Aminoacyl tRNA synthetases, Class II

Basic information

Region (hg38): 2:222566898-222656092

Previous symbols: [ "FARSLB" ]

Links

ENSG00000116120 ∙ NCBI:10056 ∙ OMIM:609690 ∙ HGNC:17800 ∙ Uniprot:Q9NSD9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Rajab interstitial lung disease with brain calcifications 1 (Strong), mode of inheritance: AR
• Rajab interstitial lung disease with brain calcifications 1 (Moderate), mode of inheritance: AR
• Rajab interstitial lung disease with brain calcifications 1 (Supportive), mode of inheritance: AR
• Rajab interstitial lung disease with brain calcifications 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Rajab interstitial lung disease with brain calcifications	AR	Cardiovascular; Pulmonary	The condition can include vascular aneurysms as well as severe lung disease, and awareness may allow prompt diagnosis and management; lung transplant has been described	Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Pulmonary; Renal	29573043

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FARSB gene.

• not provided (115 variants)
• Inborn genetic diseases (23 variants)
• Rajab interstitial lung disease with brain calcifications (6 variants)
• Rajab interstitial lung disease with brain calcifications 1 (4 variants)
• Cirrhosis of liver;Vascular dilatation;Cerebral calcification;Interstitial pneumonitis (2 variants)
• Cirrhosis of liver;Interstitial pneumonitis;Cerebral calcification;Vascular dilatation (2 variants)
• FARSB-related condition (1 variants)
• Severe early-onset pulmonary alveolar proteinosis due to MARS deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FARSB gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				23	4	27
missense	5	1	63	3	3	75
nonsense			1			1
start loss			1			1
frameshift	3					3
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			2	1	2	5
non coding				18	2	20
Total	8	2	65	44	9

Highest pathogenic variant AF is 0.00000657

Variants in FARSB

This is a list of pathogenic ClinVar variants found in the FARSB region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-222571867-A-G		FARSB-related disorder	Benign (Nov 21, 2023)
2-222571884-C-A			Uncertain significance (Nov 29, 2022)
2-222571888-C-T		FARSB-related disorder	Benign (Jan 31, 2024)
2-222571891-T-C			Uncertain significance (May 10, 2023)
2-222571898-T-C			Likely benign (Nov 28, 2023)
2-222571915-T-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
2-222571921-G-A			Likely benign (Jul 12, 2022)
2-222571939-C-T			Uncertain significance (Nov 27, 2023)
2-222571940-G-A		FARSB-related disorder	Likely benign (Oct 13, 2023)
2-222571948-G-A			Uncertain significance (Aug 21, 2022)
2-222571967-G-A			Likely benign (Oct 19, 2022)
2-222571969-C-T		Inborn genetic diseases	Likely benign (Jun 29, 2023)
2-222571973-T-C			Likely benign (Jul 01, 2022)
2-222571977-C-A			Uncertain significance (Aug 01, 2023)
2-222571990-T-C			Uncertain significance (Aug 03, 2022)
2-222572000-T-G		FARSB-related disorder	Benign/Likely benign (Oct 27, 2023)
2-222572002-G-A			Uncertain significance (Aug 05, 2022)
2-222572006-G-A			Likely benign (Jun 29, 2022)
2-222572031-G-C		FARSB-related disorder	Likely benign (Aug 25, 2023)
2-222599911-C-T		Rajab interstitial lung disease with brain calcifications 1	Benign/Likely benign (Nov 27, 2023)
2-222599966-C-G			Uncertain significance (Mar 14, 2022)
2-222599970-G-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
2-222599972-G-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
2-222600017-A-C			Uncertain significance (Mar 18, 2022)
2-222600042-A-G			Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FARSB	protein_coding	protein_coding	ENST00000281828	17	85802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00330	0.997	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	259	317	0.817	0.0000160	3858
Missense in Polyphen		51	91.698	0.55617		1140
Synonymous	0.716	103	113	0.914	0.00000600	1125
Loss of Function	3.43	10	30.4	0.329	0.00000167	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000386	0.000310
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000236	0.000229
Middle Eastern	0.000109	0.000109
South Asian	0.0000328	0.0000327
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Aminoacyl-tRNA biosynthesis - Homo sapiens (human);Phenylalanine and Tyrosine Metabolism;Phenylketonuria;Tyrosinemia Type 3 (TYRO3);Tyrosinemia Type 2 (or Richner-Hanhart syndrome);Amino Acid metabolism;tRNA Aminoacylation;Translation;Metabolism of proteins;tRNA charging;Cytosolic tRNA aminoacylation (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.279
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.651
• hipred: Y
• hipred_score: 0.653
• ghis: 0.612

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Farsb

Gene ontology

• Biological process: translation;phenylalanyl-tRNA aminoacylation;protein heterotetramerization
• Cellular component: cytoplasm;cytosol;phenylalanine-tRNA ligase complex;membrane
• Molecular function: magnesium ion binding;RNA binding;phenylalanine-tRNA ligase activity;protein binding;ATP binding