ATE1

arginyltransferase 1

Basic information

Region (hg38): 10:121709393-121928801

Links

ENSG00000107669 ∙ NCBI:11101 ∙ OMIM:607103 ∙ HGNC:782 ∙ Uniprot:O95260 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital heart disease (Disputed Evidence), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATE1 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				3	4	7
missense			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	28	3	5

Variants in ATE1

This is a list of pathogenic ClinVar variants found in the ATE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-121743672-T-C		ATE1-related disorder	Benign (Oct 28, 2019)
10-121743706-C-T		not specified	Uncertain significance (May 27, 2022)
10-121743745-C-A		not specified	Uncertain significance (Jan 30, 2024)
10-121743784-A-G		not specified	Uncertain significance (Jun 22, 2021)
10-121743840-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-121790175-C-T		not specified	Uncertain significance (Dec 19, 2023)
10-121790176-T-G		ATE1-related disorder	Benign (Oct 17, 2019)
10-121790183-T-C		not specified	Uncertain significance (May 09, 2022)
10-121790195-C-A		not specified	Uncertain significance (Oct 05, 2022)
10-121790234-A-G		not specified	Uncertain significance (Mar 19, 2024)
10-121836739-T-C		ATE1-related disorder	Benign (Oct 17, 2019)
10-121841075-A-G		ATE1-related disorder	Benign (Oct 28, 2019)
10-121841098-C-T		not specified	Uncertain significance (Jul 05, 2023)
10-121841103-A-C		not specified	Uncertain significance (Nov 10, 2022)
10-121841121-T-C		not specified	Uncertain significance (Sep 20, 2023)
10-121841155-A-C		not specified	Uncertain significance (Mar 25, 2024)
10-121841168-G-A		ATE1-related disorder	Likely benign (Mar 12, 2019)
10-121841216-G-C		not specified	Uncertain significance (Jul 19, 2023)
10-121841263-C-T		not specified	Uncertain significance (Nov 10, 2022)
10-121898862-G-A		ATE1-related disorder	Likely benign (May 06, 2019)
10-121899882-G-A		not specified	Uncertain significance (Jun 22, 2023)
10-121899918-C-T		not specified	Uncertain significance (Jun 04, 2024)
10-121899936-G-A		not specified	Uncertain significance (Aug 28, 2023)
10-121899963-G-A		not specified	Uncertain significance (Nov 15, 2021)
10-121902393-C-G		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATE1	protein_coding	protein_coding	ENST00000369043	12	188378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0406	0.959	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.634	244	274	0.892	0.0000138	3392
Missense in Polyphen		40	74.765	0.53501		910
Synonymous	-0.989	112	99.5	1.13	0.00000553	911
Loss of Function	3.85	9	32.8	0.275	0.00000187	386

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000180	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the post-translational conjugation of arginine to the N-terminal aspartate or glutamate of a protein. This arginylation is required for degradation of the protein via the ubiquitin pathway. Does not arginylate cysteine residues (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 0.364
• hipred: N
• hipred_score: 0.414
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.823

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ate1
• Phenotype: craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: proteasomal protein catabolic process;protein arginylation
• Cellular component: nucleus;cytoplasm
• Molecular function: arginyltransferase activity;protein binding