AMD1

adenosylmethionine decarboxylase 1

Basic information

Region (hg38): 6:110874769-110898879

Links

ENSG00000123505 ∙ NCBI:262 ∙ OMIM:180980 ∙ HGNC:457 ∙ Uniprot:P17707 ∙ 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 AMD1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMD1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in AMD1

This is a list of pathogenic ClinVar variants found in the AMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-110887569-A-C		not specified	Uncertain significance (Dec 20, 2022)
6-110888913-C-A		not specified	Uncertain significance (Jul 22, 2022)
6-110888948-C-A		not specified	Uncertain significance (May 05, 2023)
6-110890330-T-C		not specified	Uncertain significance (Nov 15, 2023)
6-110892914-C-T		not specified	Uncertain significance (Jul 20, 2022)
6-110893531-G-A		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMD1	protein_coding	protein_coding	ENST00000368885	9	20944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0177	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	100	186	0.537	0.00000955	2241
Missense in Polyphen		12	49.598	0.24194		711
Synonymous	0.537	55	60.3	0.912	0.00000285	595
Loss of Function	3.56	1	16.7	0.0599	7.04e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000170	0.000166
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000279	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000221	0.000196
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for biosynthesis of the polyamines spermidine and spermine. Promotes maintenance and self-renewal of embryonic stem cells, by maintaining spermine levels. {ECO:0000250|UniProtKB:P0DMN7}.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;Spermidine and Spermine Biosynthesis;Cystathionine Beta-Synthase Deficiency;Methionine De Novo and Salvage Pathway;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;spermidine biosynthesis;methionine salvage cycle III;spermine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.290

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.766
• hipred: Y
• hipred_score: 0.626
• ghis: 0.597

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.897

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amd1
• Phenotype: embryo 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)

Gene ontology

• Biological process: S-adenosylmethioninamine biosynthetic process;polyamine metabolic process;spermine biosynthetic process;spermidine biosynthetic process;S-adenosylmethionine metabolic process
• Cellular component: cytosol
• Molecular function: adenosylmethionine decarboxylase activity;putrescine binding