AARSD1

alanyl-tRNA synthetase domain containing 1

Basic information

Region (hg38): 17:42950525-42964498

Links

ENSG00000266967 ∙ NCBI:80755 ∙ OMIM:613212 ∙ HGNC:28417 ∙ Uniprot:Q9BTE6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AARSD1 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AARSD1 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						0
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in AARSD1

This is a list of pathogenic ClinVar variants found in the AARSD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42950612-G-A		not specified	Uncertain significance (Mar 22, 2022)
17-42950613-T-C		not specified	Uncertain significance (Jun 10, 2022)
17-42950636-G-A		not specified	Uncertain significance (Jul 20, 2022)
17-42950649-T-G		not specified	Uncertain significance (Dec 09, 2023)
17-42950655-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-42950672-T-A		not specified	Uncertain significance (Sep 29, 2023)
17-42950685-G-A		not specified	Uncertain significance (Jul 14, 2021)
17-42950728-C-G		not specified	Uncertain significance (Jun 29, 2023)
17-42951854-C-A		not specified	Uncertain significance (Jan 11, 2023)
17-42951854-C-G		not specified	Likely benign (Feb 17, 2024)
17-42951879-A-C		not specified	Uncertain significance (Dec 28, 2022)
17-42953740-T-C		not specified	Uncertain significance (Oct 12, 2022)
17-42954888-A-G		not specified	Uncertain significance (Feb 15, 2023)
17-42954895-C-T		not specified	Uncertain significance (Dec 09, 2023)
17-42954900-C-A		not specified	Uncertain significance (Jun 01, 2023)
17-42954924-T-C		not specified	Uncertain significance (Oct 10, 2023)
17-42954943-G-C		not specified	Uncertain significance (Jun 21, 2023)
17-42955851-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-42956232-G-C		not specified	Uncertain significance (Aug 02, 2021)
17-42956286-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-42956310-C-T		not specified	Uncertain significance (May 31, 2023)
17-42956415-C-T		not specified	Uncertain significance (Feb 14, 2024)
17-42956499-C-T		not specified	Uncertain significance (Dec 21, 2022)
17-42957163-G-T		not specified	Uncertain significance (May 18, 2022)
17-42961203-T-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AARSD1	protein_coding	protein_coding	ENST00000427569	12	13973

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.07e-9	0.571	125513	0	235	125748	0.000935

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00928	243	243	0.998	0.0000136	2699
Missense in Polyphen		50	56.694	0.88192		609
Synonymous	-0.165	94	92.0	1.02	0.00000485	823
Loss of Function	1.18	16	21.9	0.729	0.00000102	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00767	0.00769
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000291	0.000290
Middle Eastern	0.000272	0.000272
South Asian	0.00173	0.00173
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions in trans to edit the amino acid moiety from incorrectly charged tRNA(Ala). {ECO:0000250}.

Recessive Scores

• pRec: 0.0878

Intolerance Scores

• loftool: 0.310
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.131
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0537

Mouse Genome Informatics

• Gene name: Aarsd1

Gene ontology

• Biological process: alanyl-tRNA aminoacylation;regulation of translational fidelity;biological_process;aminoacyl-tRNA metabolism involved in translational fidelity
• Cellular component: nucleus;cytoplasm
• Molecular function: Ser-tRNA(Ala) hydrolase activity;molecular_function;nucleic acid binding;alanine-tRNA ligase activity;ATP binding;metal ion binding