ADI1

acireductone dioxygenase 1

Basic information

Region (hg38): 2:3497366-3519531

Links

ENSG00000182551 ∙ NCBI:55256 ∙ OMIM:613400 ∙ HGNC:30576 ∙ Uniprot:Q9BV57 ∙ 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 ADI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADI1 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			7	2		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in ADI1

This is a list of pathogenic ClinVar variants found in the ADI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-3499025-G-A		not specified	Uncertain significance (Jul 06, 2021)
2-3499049-C-G		not specified	Uncertain significance (Oct 12, 2021)
2-3499075-G-A		not specified	Uncertain significance (Mar 07, 2024)
2-3499076-T-C		not specified	Likely benign (Sep 15, 2021)
2-3500939-G-C		not specified	Uncertain significance (Jan 10, 2023)
2-3519384-C-G		not specified	Uncertain significance (Jul 17, 2023)
2-3519408-C-G		not specified	Uncertain significance (Sep 15, 2021)
2-3519448-G-C		not specified	Uncertain significance (Aug 22, 2023)
2-3519461-G-C		not specified	Likely benign (May 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADI1	protein_coding	protein_coding	ENST00000327435	4	22376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000315	0.360	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.199	99	105	0.945	0.00000682	1175
Missense in Polyphen		41	45.456	0.90197		491
Synonymous	0.897	36	43.5	0.827	0.00000325	318
Loss of Function	0.147	7	7.43	0.942	4.00e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000664	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of formate and 2-keto-4- methylthiobutyrate (KMTB) from 1,2-dihydroxy-3-keto-5- methylthiopentene (DHK-MTPene). Also down-regulates cell migration mediated by MMP14. Necessary for hepatitis C virus replication in an otherwise non-permissive cell line. {ECO:0000255|HAMAP- Rule:MF_03154, ECO:0000269|PubMed:11602742, ECO:0000269|PubMed:15938715}.
• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Methionine De Novo and Salvage Pathway;Metabolism of polyamines;Metabolism of amino acids and derivatives;Methionine salvage pathway;Metabolism;<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation;<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation;methionine salvage cycle III;Sulfur amino acid metabolism (Consensus)

Recessive Scores

• pRec: 0.248

Intolerance Scores

• loftool: 0.293
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.228
• hipred: N
• hipred_score: 0.394
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adi1

Gene ontology

• Biological process: methionine metabolic process;L-methionine salvage from methylthioadenosine;oxidation-reduction process
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane
• Molecular function: iron ion binding;protein binding;acireductone dioxygenase [iron(II)-requiring] activity;oxidoreductase activity