AFMID

arylformamidase

Basic information

Region (hg38): 17:78187358-78207702

Links

ENSG00000183077 ∙ NCBI:125061 ∙ ∙ HGNC:20910 ∙ Uniprot:Q63HM1 ∙ 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 AFMID gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFMID 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				2		2
missense			24	2		26
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	4	0

Variants in AFMID

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

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

Position	Type	Phenotype	Significance	ClinVar
17-78187374-A-G		not specified	Uncertain significance (Nov 13, 2023)
17-78191004-T-C		not specified	Uncertain significance (Oct 12, 2021)
17-78191010-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-78202595-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-78202747-G-A		not specified	Uncertain significance (Mar 21, 2023)
17-78204678-G-C		not specified	Uncertain significance (Aug 12, 2021)
17-78204724-A-G		not specified	Uncertain significance (May 27, 2022)
17-78204726-G-A		not specified	Uncertain significance (Apr 13, 2023)
17-78204831-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-78204840-A-G		not specified	Uncertain significance (Jan 20, 2023)
17-78204851-C-A		not specified	Uncertain significance (Aug 13, 2021)
17-78205145-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-78205451-G-A		not specified	Uncertain significance (Apr 10, 2023)
17-78205451-G-C		not specified	Uncertain significance (Jun 18, 2021)
17-78205481-G-A		not specified	Likely benign (Aug 12, 2021)
17-78205487-A-G		not specified	Uncertain significance (Dec 02, 2022)
17-78205492-A-G			Likely benign (May 01, 2022)
17-78205653-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-78205671-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-78205685-G-A		not specified	Uncertain significance (Nov 15, 2023)
17-78205698-A-T		not specified	Uncertain significance (Jan 26, 2022)
17-78205962-A-G		not specified	Likely benign (Dec 09, 2023)
17-78206002-C-G		not specified	Uncertain significance (Sep 25, 2023)
17-78206009-A-G		not specified	Uncertain significance (Jun 29, 2022)
17-78206026-C-T			Likely benign (Apr 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFMID	protein_coding	protein_coding	ENST00000327898	11	20385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.50e-9	0.593	125295	2	451	125748	0.00180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.124	181	186	0.974	0.0000108	1995
Missense in Polyphen		59	60.208	0.97994		648
Synonymous	0.224	77	79.5	0.968	0.00000565	589
Loss of Function	1.20	16	22.1	0.724	0.00000120	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00243	0.00243
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000326	0.000326
Finnish	0.000284	0.000277
European (Non-Finnish)	0.00310	0.00308
Middle Eastern	0.000326	0.000326
South Asian	0.000426	0.000425
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation. Kynurenine may be further oxidized to nicotinic acid, NAD(H) and NADP(H). Required for elimination of toxic metabolites. {ECO:0000255|HAMAP-Rule:MF_03014}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Tryptophan Metabolism;NAD Biosynthesis II (from tryptophan);Tryptophan metabolism;Tryptophan catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde;Metabolism;L-kynurenine degradation;NAD <i>de novo</i> biosynthesis;Tryptophan degradation;superpathway of tryptophan utilization;tryptophan degradation (Consensus)

Recessive Scores

• pRec: 0.218

Intolerance Scores

• loftool: 0.378
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.0656
• hipred: N
• hipred_score: 0.169
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Afmid
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; renal/urinary system phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: tryptophan catabolic process to kynurenine;'de novo' NAD biosynthetic process from tryptophan
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: arylformamidase activity