AMDHD1

amidohydrolase domain containing 1, the group of M38 metallopeptidases

Basic information

Region (hg38): 12:95943331-95968720

Links

ENSG00000139344 ∙ NCBI:144193 ∙ ∙ HGNC:28577 ∙ Uniprot:Q96NU7 ∙ 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 AMDHD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMDHD1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in AMDHD1

This is a list of pathogenic ClinVar variants found in the AMDHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-95943430-A-C		not specified	Uncertain significance (Apr 09, 2024)
12-95943501-G-T		not specified	Uncertain significance (Nov 06, 2023)
12-95943528-G-T		not specified	Uncertain significance (Jul 13, 2021)
12-95956701-A-G		not specified	Uncertain significance (Aug 02, 2021)
12-95956715-C-G		not specified	Uncertain significance (Jul 19, 2023)
12-95956790-C-A		not specified	Uncertain significance (Mar 14, 2023)
12-95956793-C-G		not specified	Uncertain significance (Nov 13, 2023)
12-95956808-A-G		not specified	Uncertain significance (Oct 12, 2022)
12-95956882-G-A		not specified	Uncertain significance (Dec 05, 2022)
12-95960454-T-G		not specified	Uncertain significance (Feb 09, 2022)
12-95960478-A-G		not specified	Uncertain significance (May 11, 2022)
12-95960486-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-95960501-G-A		not specified	Uncertain significance (May 27, 2022)
12-95960517-G-A		not specified	Uncertain significance (Jul 12, 2023)
12-95960529-T-C		not specified	Uncertain significance (Mar 15, 2024)
12-95965726-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-95965763-C-T		not specified	Uncertain significance (Jan 23, 2024)
12-95966433-C-T		not specified	Uncertain significance (May 24, 2023)
12-95966442-A-G		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMDHD1	protein_coding	protein_coding	ENST00000266736	9	25300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.13e-8	0.531	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.304	254	241	1.06	0.0000139	2754
Missense in Polyphen		92	98.751	0.93164		1070
Synonymous	0.769	84	93.5	0.899	0.00000597	838
Loss of Function	1.02	14	18.8	0.746	9.47e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000486	0.000485
Ashkenazi Jewish	0.00	0.00
East Asian	0.00147	0.00147
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000202	0.000202
Middle Eastern	0.00147	0.00147
South Asian	0.000341	0.000327
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Histidine metabolism - Homo sapiens (human);Histidine Metabolism;Histidinemia;Histidine catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Metabolism;histidine degradation (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.793
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.406
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.312

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amdhd1

Gene ontology

• Biological process: histidine catabolic process;histidine catabolic process to glutamate and formamide;histidine catabolic process to glutamate and formate
• Cellular component: cytosol
• Molecular function: molecular_function;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides;metal ion binding;imidazolonepropionase activity