IL4I1

interleukin 4 induced 1

Basic information

Region (hg38): 19:49889654-49929539

Links

ENSG00000104951 ∙ NCBI:259307 ∙ OMIM:609742 ∙ HGNC:19094 ∙ Uniprot:Q96RQ9 ∙ 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 IL4I1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL4I1 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			122	52	16	190
Total	0	0	161	53	16

Variants in IL4I1

This is a list of pathogenic ClinVar variants found in the IL4I1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49889686-G-C		not specified	Uncertain significance (Sep 09, 2024)
19-49889709-T-G		not specified	Uncertain significance (Aug 17, 2021)
19-49889729-G-A		not specified	Uncertain significance (Sep 28, 2022)
19-49889741-C-G		not specified	Uncertain significance (Dec 02, 2024)
19-49889762-A-C		not specified	Uncertain significance (Jul 06, 2022)
19-49889845-G-T		not specified	Uncertain significance (Mar 01, 2024)
19-49889849-C-G		not specified	Uncertain significance (Jan 23, 2024)
19-49889866-T-C		not specified	Likely benign (Mar 28, 2024)
19-49889885-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-49889959-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-49889981-C-T		not specified	Uncertain significance (Jan 01, 2025)
19-49890065-C-G		not specified	Uncertain significance (Mar 31, 2024)
19-49890118-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-49890137-C-T		not specified	Uncertain significance (Feb 20, 2025)
19-49890188-C-T		not specified	Uncertain significance (Apr 28, 2022)
19-49890262-C-T		not specified	Uncertain significance (Oct 10, 2023)
19-49890266-C-T		not specified	Uncertain significance (May 27, 2022)
19-49890280-C-A		not specified	Uncertain significance (Oct 27, 2021)
19-49890289-G-A		not specified	Uncertain significance (Jun 06, 2022)
19-49890497-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-49890562-C-G		not specified	Uncertain significance (Mar 08, 2025)
19-49890592-C-A		not specified	Uncertain significance (Aug 19, 2024)
19-49890978-T-C		not specified	Uncertain significance (May 18, 2022)
19-49891058-A-G		not specified	Uncertain significance (Nov 28, 2024)
19-49891088-C-G		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL4I1	protein_coding	protein_coding	ENST00000595948	7	39886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00396	0.962	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	276	373	0.741	0.0000222	3786
Missense in Polyphen		95	159.09	0.59715		1515
Synonymous	0.278	170	175	0.973	0.0000119	1212
Loss of Function	1.86	6	13.3	0.450	5.73e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000395	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lysosomal L-amino-acid oxidase with highest specific activity with phenylalanine. May play a role in lysosomal antigen processing and presentation (By similarity). {ECO:0000250}.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Tryptophan metabolism - Homo sapiens (human);Phenylalanine metabolism - Homo sapiens (human);Phenylalanine, tyrosine and tryptophan biosynthesis - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Tyrosine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Phenylalanine and Tyrosine Metabolism;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Hypoacetylaspartia;Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;Aspartate Metabolism;Phenylketonuria;Tyrosinemia Type 3 (TYRO3);Tyrosinemia Type 2 (or Richner-Hanhart syndrome);Canavan Disease;Cystathionine Beta-Synthase Deficiency;Methionine De Novo and Salvage Pathway;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Tyrosine metabolism;Phenylalanine and tyrosine catabolism;Metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.119
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.61

Haploinsufficiency Scores

• pHI: 0.0558
• hipred: N
• hipred_score: 0.455
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.698

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il4i1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: L-phenylalanine catabolic process;cellular amino acid catabolic process;oxidation-reduction process
• Cellular component: extracellular region;lysosome
• Molecular function: L-amino-acid oxidase activity;oxidoreductase activity