MACROD2

mono-ADP ribosylhydrolase 2, the group of Macro domain containing

Basic information

Region (hg38): 20:13995368-16053197

Previous symbols: [ "C20orf133" ]

Links

ENSG00000172264 ∙ NCBI:140733 ∙ OMIM:611567 ∙ HGNC:16126 ∙ Uniprot:A1Z1Q3 ∙ 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 MACROD2 gene.

• not provided (32 variants)
• Inborn genetic diseases (26 variants)
• Hypogonadotropic hypogonadism 21 with or without anosmia (4 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MACROD2 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				2		2
missense			11	3	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			24	13	7	44
Total	0	0	35	18	8

Variants in MACROD2

This is a list of pathogenic ClinVar variants found in the MACROD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-13995758-G-A		MACROD2-related disorder	Benign (May 28, 2019)
20-14002344-A-T		not specified	Uncertain significance (Sep 22, 2022)
20-14002355-C-A		not specified	Uncertain significance (Aug 02, 2023)
20-14085630-C-T		MACROD2-related disorder	Benign (Oct 18, 2019)
20-14325600-T-C			Uncertain significance (Nov 16, 2023)
20-14325601-A-G		not specified	Uncertain significance (Jan 22, 2024)
20-14325642-A-G		not specified	Uncertain significance (Feb 05, 2024)
20-14325678-A-G			Uncertain significance (May 01, 2020)
20-14325715-G-A		not specified	Uncertain significance (Oct 26, 2022)
20-14325780-G-A		Hypogonadotropic hypogonadism 21 with or without anosmia	Uncertain significance (Dec 24, 2020)
20-14325865-C-G		High myopia	Uncertain significance (Dec 17, 2018)
20-14325903-C-A		not specified	Uncertain significance (Feb 28, 2023)
20-14325997-G-A		not specified	Uncertain significance (May 18, 2023)
20-14326062-A-T		not specified	Uncertain significance (Nov 09, 2021)
20-14326111-C-G		FLRT3-related disorder • not specified	Uncertain significance (Feb 07, 2024)
20-14326125-C-T			Uncertain significance (Jan 02, 2024)
20-14326127-T-G			Benign (Jan 29, 2024)
20-14326153-T-C			Uncertain significance (May 20, 2020)
20-14326168-G-C		not specified	Uncertain significance (Jan 08, 2024)
20-14326180-G-A		FLRT3-related disorder	Likely benign (Oct 14, 2020)
20-14326184-A-G			Benign (Jan 22, 2024)
20-14326250-G-A		Hypogonadotropic hypogonadism 21 with or without anosmia	Benign (Jan 31, 2024)
20-14326252-T-A		Hypogonadotropic hypogonadism 21 with or without anosmia	Uncertain significance (Aug 22, 2022)
20-14326305-T-A		Amenorrhea	Uncertain significance (Mar 08, 2021)
20-14326307-G-T			Benign (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MACROD2	protein_coding	protein_coding	ENST00000217246	17	2057828

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.435	0.565	125727	0	11	125738	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.708	196	226	0.867	0.0000114	2819
Missense in Polyphen		61	88.529	0.68904		1114
Synonymous	0.794	72	81.1	0.888	0.00000458	726
Loss of Function	3.78	6	27.3	0.220	0.00000123	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000274	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.000274	0.000272
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Removes ADP-ribose from glutamate residues in proteins bearing a single ADP-ribose moiety. Inactive towards proteins bearing poly-ADP-ribose. Deacetylates O-acetyl-ADP ribose, a signaling molecule generated by the deacetylation of acetylated lysine residues in histones and other proteins. {ECO:0000269|PubMed:21257746, ECO:0000269|PubMed:23474712}.

Intolerance Scores

• loftool: 0.705
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.284
• hipred: N
• hipred_score: 0.331
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.336

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Macrod2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; vision/eye 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); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular response to DNA damage stimulus;brain development;response to bacterium;purine nucleoside metabolic process;protein de-ADP-ribosylation
• Cellular component: nucleus;nucleolus;centrosome
• Molecular function: hydrolase activity, acting on glycosyl bonds;deacetylase activity