AMPD3

adenosine monophosphate deaminase 3, the group of Adenosine deaminase family

Basic information

Region (hg38): 11:10308312-10507579

Links

ENSG00000133805 ∙ NCBI:272 ∙ OMIM:102772 ∙ HGNC:470 ∙ Uniprot:Q01432 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• adenosine monophosphate deaminase deficiency (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Erythrocytic AMP deaminase deficiency	AD/AR	General	The condition may not be clinically relevant	General	3804327; 7881427; 8004104

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AMPD3 gene.

• Erythrocyte AMP deaminase deficiency (111 variants)
• Inborn genetic diseases (23 variants)
• not provided (15 variants)
• not specified (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMPD3 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			15	5	3	23
missense	1		59	3	1	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			5			5
non coding			29	1	12	42
Total	1	0	103	9	16

Highest pathogenic variant AF is 0.000151

Variants in AMPD3

This is a list of pathogenic ClinVar variants found in the AMPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-10455142-A-G		Erythrocyte AMP deaminase deficiency	Benign (Jan 13, 2018)
11-10455151-C-T		Erythrocyte AMP deaminase deficiency	Benign (Jan 13, 2018)
11-10455191-T-C		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 12, 2018)
11-10455214-A-G		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 13, 2018)
11-10455215-G-C		Erythrocyte AMP deaminase deficiency	Benign (Jan 12, 2018)
11-10455254-G-A		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 13, 2018)
11-10455297-T-C			Uncertain significance (Nov 03, 2021)
11-10455338-A-C		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 12, 2018)
11-10455351-T-C		Erythrocyte AMP deaminase deficiency	Benign (Jan 12, 2018)
11-10455366-G-T		Erythrocyte AMP deaminase deficiency	Benign (Jan 13, 2018)
11-10455372-T-G		Erythrocyte AMP deaminase deficiency	Benign (Jan 12, 2018)
11-10455403-AGCCAGC-A		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jun 14, 2016)
11-10455429-C-T		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 13, 2018)
11-10455445-G-A		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 12, 2018)
11-10456392-G-T		AMPD3-related disorder	Likely benign (Jan 04, 2021)
11-10461509-T-G		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 12, 2018)
11-10461524-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-10461526-C-T		Erythrocyte AMP deaminase deficiency	Uncertain significance (Apr 27, 2017)
11-10461575-T-C		Erythrocyte AMP deaminase deficiency	Uncertain significance (Mar 02, 2018)
11-10461582-G-A		AMPD3-related disorder	Likely benign (Feb 20, 2019)
11-10461600-A-C		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 12, 2018)
11-10461608-G-A		not specified	Uncertain significance (Dec 01, 2023)
11-10461629-C-T		Erythrocyte AMP deaminase deficiency	Uncertain significance (Jan 13, 2018)
11-10461728-A-G		not specified	Uncertain significance (Jan 03, 2022)
11-10461733-G-A		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMPD3	protein_coding	protein_coding	ENST00000396554	15	199267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-12	0.905	125562	0	186	125748	0.000740

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.667	416	456	0.912	0.0000303	5121
Missense in Polyphen		184	203.2	0.90549		2242
Synonymous	-0.935	206	190	1.09	0.0000128	1488
Loss of Function	2.02	25	38.5	0.649	0.00000218	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00205	0.00205
Ashkenazi Jewish	0.00	0.00
East Asian	0.00179	0.00180
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000397	0.000396
Middle Eastern	0.00179	0.00180
South Asian	0.000686	0.000686
Other	0.00212	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: AMP deaminase plays a critical role in energy metabolism.
• Disease: DISEASE: Adenosine monophosphate deaminase deficiency erythrocyte type (AMPDDE) [MIM:612874]: A metabolic disorder due to lack of activity of the erythrocyte isoform of AMP deaminase. It is a clinically asymptomatic condition characterized by a 50% increase in steady-state levels of ATP in affected cells. Individuals with complete deficiency of erythrocyte AMP deaminase are healthy and have no hematologic disorders. {ECO:0000269|PubMed:11139257, ECO:0000269|PubMed:7881427, ECO:0000269|PubMed:8004104, ECO:0000269|PubMed:9598089}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Purine metabolism - Homo sapiens (human);Neutrophil degranulation;Metabolism of nucleotides;Innate Immune System;Immune System;Metabolism;Nucleotide salvage;Purine salvage;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.307

Intolerance Scores

• loftool: 0.0203
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.74

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.455
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.241

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ampd3
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); hematopoietic system phenotype

Gene ontology

• Biological process: AMP catabolic process;IMP salvage;erythrocyte homeostasis;purine-containing compound salvage;neutrophil degranulation;ADP metabolic process;ATP metabolic process;GTP metabolic process;energy homeostasis
• Cellular component: extracellular region;cytosol;secretory granule lumen;ficolin-1-rich granule lumen
• Molecular function: AMP deaminase activity;protein binding;metal ion binding