AMDHD2

amidohydrolase domain containing 2

Basic information

Region (hg38): 16:2520357-2531422

Links

ENSG00000162066 ∙ NCBI:51005 ∙ ∙ HGNC:24262 ∙ Uniprot:Q9Y303 ∙ 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 AMDHD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMDHD2 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				1		1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	3		18
Total	0	0	35	4	0

Variants in AMDHD2

This is a list of pathogenic ClinVar variants found in the AMDHD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2520486-G-A		not specified	Uncertain significance (Dec 01, 2022)
16-2520487-C-T		not specified	Uncertain significance (Aug 30, 2022)
16-2520489-C-T		not specified	Uncertain significance (Aug 04, 2023)
16-2520887-A-G		not specified	Uncertain significance (Nov 07, 2023)
16-2521013-A-T		not specified	Uncertain significance (Jun 22, 2021)
16-2521016-G-A		not specified	Uncertain significance (Apr 04, 2023)
16-2521049-C-T		not specified	Uncertain significance (Sep 06, 2022)
16-2521089-C-T		not specified	Uncertain significance (Sep 14, 2023)
16-2527603-G-T		not specified	Uncertain significance (May 30, 2023)
16-2527803-G-A		not specified	Uncertain significance (Jun 21, 2023)
16-2527826-G-A		not specified	Uncertain significance (Mar 13, 2023)
16-2527842-C-T		not specified	Uncertain significance (Jun 01, 2023)
16-2527913-C-T			Likely benign (Jun 01, 2022)
16-2527974-G-C		not specified	Uncertain significance (May 08, 2024)
16-2528245-C-T		not specified	Uncertain significance (Mar 23, 2023)
16-2528365-C-T		not specified	Uncertain significance (Nov 09, 2021)
16-2528463-G-A		not specified	Uncertain significance (Apr 04, 2024)
16-2528497-A-G		not specified	Uncertain significance (Aug 15, 2023)
16-2528566-G-A		not specified	Uncertain significance (Oct 30, 2023)
16-2528616-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-2528679-C-G		not specified	Uncertain significance (Aug 12, 2022)
16-2528716-C-G		not specified	Uncertain significance (Sep 16, 2021)
16-2529492-G-A		not specified	Uncertain significance (May 15, 2024)
16-2529522-T-G		not specified	Uncertain significance (Aug 02, 2021)
16-2530282-C-G		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMDHD2	protein_coding	protein_coding	ENST00000413459	11	11066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00231	0.982	125675	0	25	125700	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.520	341	369	0.924	0.0000233	3732
Missense in Polyphen		79	121.27	0.65143		1220
Synonymous	-3.74	226	165	1.37	0.0000115	1313
Loss of Function	2.12	7	16.2	0.431	6.93e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000838	0.0000791
Middle Eastern	0.000111	0.000109
South Asian	0.000360	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes the N-glycolyl group from N- glycolylglucosamine 6-phosphate (GlcNGc-6-P) in the N- glycolylneuraminic acid (Neu5Gc) degradation pathway. Although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded. {ECO:0000269|PubMed:22692205}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;<i>N</i>-acetylglucosamine degradation II;Post-translational protein modification;Metabolism of proteins;<i>N</i>-acetylglucosamine degradation I;Synthesis of UDP-N-acetyl-glucosamine;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.198
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.21

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.187
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amdhd2

Gene ontology

• Biological process: carbohydrate metabolic process;N-acetylglucosamine catabolic process;UDP-N-acetylglucosamine biosynthetic process;N-acetylneuraminate catabolic process
• Cellular component: nucleus;cytosol
• Molecular function: protein binding;N-acetylglucosamine-6-phosphate deacetylase activity;metal ion binding;N-acetylgalactosamine-6-phosphate deacetylase activity