ADPRM

ADP-ribose/CDP-alcohol diphosphatase, manganese dependent, the group of Sugar phosphatases

Basic information

Region (hg38): 17:10697594-10711558

Previous symbols: [ "C17orf48" ]

Links

ENSG00000170222 ∙ NCBI:56985 ∙ ∙ HGNC:30925 ∙ Uniprot:Q3LIE5 ∙ 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 ADPRM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADPRM 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	4	6
Total	0	0	13	2	4

Variants in ADPRM

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

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

Position	Type	Phenotype	Significance	ClinVar
17-10697598-G-A			Benign (Jun 19, 2018)
17-10697654-G-A			Benign (Jun 19, 2018)
17-10697719-T-G			Likely benign (Jun 29, 2018)
17-10697743-G-C			Benign (Jun 19, 2018)
17-10697803-C-T			Likely benign (Oct 05, 2018)
17-10697816-C-CG			Benign (Jun 14, 2018)
17-10704939-C-A		not specified	Uncertain significance (Oct 01, 2024)
17-10704939-C-T		not specified	Uncertain significance (Apr 06, 2023)
17-10704972-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-10705031-T-A		not specified	Uncertain significance (Mar 18, 2024)
17-10705050-C-T		not specified	Uncertain significance (Jun 04, 2024)
17-10705079-C-A		not specified	Uncertain significance (Jan 31, 2024)
17-10705143-G-A		not specified	Uncertain significance (Jun 22, 2023)
17-10705166-T-A		not specified	Uncertain significance (Dec 11, 2023)
17-10705182-T-C		not specified	Uncertain significance (Oct 03, 2024)
17-10705500-C-G		not specified	Uncertain significance (Sep 03, 2024)
17-10710857-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-10710861-C-G		not specified	Uncertain significance (Nov 27, 2023)
17-10710917-C-G		not specified	Uncertain significance (Apr 12, 2023)
17-10710938-T-A		not specified	Uncertain significance (Dec 19, 2023)
17-10710971-G-A		not specified	Uncertain significance (Jan 09, 2024)
17-10711086-G-A		not specified	Uncertain significance (Apr 13, 2022)
17-10711089-G-A		not specified	Uncertain significance (Apr 04, 2023)
17-10711110-T-C		not specified	Uncertain significance (Jul 26, 2024)
17-10711137-A-G		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADPRM	protein_coding	protein_coding	ENST00000379774	3	13640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000395	0.859	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	144	182	0.790	0.00000908	2301
Missense in Polyphen		40	65.169	0.61378		837
Synonymous	0.952	58	68.0	0.853	0.00000364	613
Loss of Function	1.31	7	11.9	0.590	5.91e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000786	0.000766
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.000163	0.000163
South Asian	0.000200	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes ADP-ribose, IDP-ribose, CDP-glycerol, CDP- choline and CDP-ethanolamine, but not other non-reducing ADP- sugars or CDP-glucose. May be involved in immune cell signaling as suggested by the second-messenger role of ADP-ribose, which activates TRPM2 as a mediator of oxidative/nitrosative stress (By similarity). {ECO:0000250}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Phosphate bond hydrolysis by NUDT proteins;Purine catabolism (Consensus)

Recessive Scores

• pRec: 0.0932

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.0551
• hipred: N
• hipred_score: 0.319
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adprm

Gene ontology

• Biological process: nucleobase-containing small molecule catabolic process
• Cellular component: cytosol
• Molecular function: metal ion binding;ADP-ribose diphosphatase activity;CDP-glycerol diphosphatase activity