AMPD1

adenosine monophosphate deaminase 1, the group of Adenosine deaminase family

Basic information

Region (hg38): 1:114673090-114695618

Links

ENSG00000116748 ∙ NCBI:270 ∙ OMIM:102770 ∙ HGNC:468 ∙ Uniprot:P23109 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopathy due to myoadenylate deaminase deficiency (Strong), mode of inheritance: AR
• adenosine monophosphate deaminase deficiency (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myoadenylate deaminase deficiency	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Musculoskeletal	1631143; 10086964; 10996775; 11102975; 11331279; 22538307

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMPD1 gene.

• Muscle_AMP_deaminase_deficiency (441 variants)
• Inborn_genetic_diseases (91 variants)
• not_provided (64 variants)
• not_specified (22 variants)
• AMPD1-related_disorder (13 variants)
• Autism (11 variants)
• Hypercholesterolemia,_autosomal_dominant,_type_B (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMPD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000036.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	86	10	101
missense		1	265	8		274
nonsense		2	8			10
start loss			1			1
frameshift			6	1		7
splice donor/acceptor (+/-2bp)	1		9	1		11
Total	1	3	294	96	10

Highest pathogenic variant AF is 0.000776971

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMPD1	protein_coding	protein_coding	ENST00000520113	16	22521

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.91e-21	0.00585	125491	0	257	125748	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.457	452	425	1.06	0.0000238	5208
Missense in Polyphen		211	203.92	1.0347		2407
Synonymous	-0.497	159	151	1.05	0.00000811	1426
Loss of Function	0.552	34	37.7	0.903	0.00000207	463

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00604	0.00599
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000924	0.000925
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000626	0.000624
Middle Eastern	0.000924	0.000925
South Asian	0.00140	0.00137
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: AMP deaminase plays a critical role in energy metabolism.
• Disease: DISEASE: Myopathy due to myoadenylate deaminase deficiency (MMDD) [MIM:615511]: A metabolic disorder resulting in exercise-related myopathy. It is characterized by exercise-induced muscle aches, cramps, and early fatigue. {ECO:0000269|PubMed:11102975}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Purine metabolism;Metabolism of nucleotides;Metabolism;Nucleotide salvage;Purine salvage;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.449

Intolerance Scores

• loftool: 0.126
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.17

Haploinsufficiency Scores

• pHI: 0.271
• hipred: N
• hipred_score: 0.251
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.124

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ampd1
• 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); hematopoietic 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); immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to organic substance;IMP salvage;purine-containing compound salvage
• Cellular component: cytosol
• Molecular function: AMP deaminase activity;myosin heavy chain binding;metal ion binding