DNPH1

2'-deoxynucleoside 5'-phosphate N-hydrolase 1

Basic information

Region (hg38): 6:43225629-43229481

Previous symbols: [ "C6orf108" ]

Links

ENSG00000112667 ∙ NCBI:10591 ∙ OMIM:618762 ∙ HGNC:21218 ∙ Uniprot:O43598 ∙ 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 DNPH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNPH1 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						0
Total	0	0	13	0	0

Variants in DNPH1

This is a list of pathogenic ClinVar variants found in the DNPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43225786-A-G		not specified	Uncertain significance (Jan 23, 2023)
6-43225791-C-G		not specified	Uncertain significance (Apr 04, 2023)
6-43225842-C-T		not specified	Uncertain significance (Apr 09, 2024)
6-43225843-G-A		not specified	Uncertain significance (Feb 27, 2023)
6-43225858-C-T		not specified	Uncertain significance (Jan 10, 2023)
6-43226044-T-G		not specified	Uncertain significance (Oct 04, 2022)
6-43226045-G-T		not specified	Uncertain significance (Oct 25, 2024)
6-43226063-G-T		not specified	Uncertain significance (Nov 17, 2023)
6-43226084-C-T		not specified	Uncertain significance (Mar 31, 2023)
6-43226332-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-43229269-C-T		not specified	Uncertain significance (Aug 16, 2022)
6-43229377-C-G		not specified	Uncertain significance (Sep 17, 2021)
6-43229411-C-G		not specified	Uncertain significance (Jun 10, 2024)
6-43229427-G-T		not specified	Uncertain significance (Jun 05, 2023)
6-43229438-G-C		not specified	Uncertain significance (Apr 15, 2024)
6-43229441-C-T		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNPH1	protein_coding	protein_coding	ENST00000230431	4	3856

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0321	0.828	125677	0	23	125700	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.638	78	95.5	0.816	0.00000597	1056
Missense in Polyphen		23	35.917	0.64036		399
Synonymous	-0.110	40	39.1	1.02	0.00000217	376
Loss of Function	1.16	3	6.09	0.493	2.61e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000491	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.0000975	0.0000967
Middle Eastern	0.000491	0.000489
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield deoxyribose 5- phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'- monophosphates containing purine bases are preferred to those containing pyrimidine bases. {ECO:0000255|HAMAP-Rule:MF_03036, ECO:0000269|PubMed:24260472, ECO:0000269|PubMed:25108359}.
• Pathway: Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Purine catabolism (Consensus)

Recessive Scores

• pRec: 0.152

Haploinsufficiency Scores

• pHI: 0.0728
• hipred: N
• hipred_score: 0.177
• ghis: 0.609

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	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dnph1

Gene ontology

• Biological process: purine nucleotide catabolic process;cell population proliferation;nucleoside metabolic process;deoxyribonucleoside monophosphate catabolic process;positive regulation of cell growth;epithelial cell differentiation
• Cellular component: nucleus;cytosol;extracellular exosome
• Molecular function: protein binding;identical protein binding;protein homodimerization activity;deoxyribonucleoside 5'-monophosphate N-glycosidase activity