NT5DC3

5'-nucleotidase domain containing 3

Basic information

Region (hg38): 12:103770453-103841234

Links

ENSG00000111696 ∙ NCBI:51559 ∙ OMIM:611076 ∙ HGNC:30826 ∙ Uniprot:Q86UY8 ∙ 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 NT5DC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5DC3 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in NT5DC3

This is a list of pathogenic ClinVar variants found in the NT5DC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-103777864-C-T		not specified	Likely benign (Jul 26, 2024)
12-103777941-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-103777957-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-103777971-G-T		not specified	Uncertain significance (Jan 03, 2024)
12-103777995-G-A		not specified	Uncertain significance (Jul 14, 2021)
12-103785344-T-A		not specified	Uncertain significance (Jan 23, 2024)
12-103787491-T-C		not specified	Uncertain significance (Oct 13, 2023)
12-103787508-A-C		not specified	Uncertain significance (May 20, 2024)
12-103793192-T-G		not specified	Uncertain significance (Jul 09, 2021)
12-103793207-T-C		not specified	Uncertain significance (Oct 29, 2021)
12-103793482-C-T		not specified	Uncertain significance (Feb 27, 2023)
12-103793483-G-A		not specified	Uncertain significance (Apr 18, 2023)
12-103796899-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-103796943-A-G		not specified	Uncertain significance (Jul 10, 2024)
12-103797015-G-T		not specified	Uncertain significance (May 09, 2022)
12-103798622-C-T		not specified	Uncertain significance (Nov 14, 2024)
12-103806856-C-T		not specified	Uncertain significance (Jun 18, 2024)
12-103806857-G-A		not specified	Uncertain significance (Aug 23, 2021)
12-103806881-G-A		not specified	Uncertain significance (Jun 07, 2024)
12-103814983-G-A		not specified	Uncertain significance (Jul 14, 2022)
12-103815093-C-G		not specified	Uncertain significance (Sep 03, 2024)
12-103815102-C-T		not specified	Uncertain significance (Aug 04, 2021)
12-103841009-C-T		not specified	Uncertain significance (Nov 10, 2024)
12-103841029-A-C		not specified	Uncertain significance (Aug 04, 2021)
12-103841030-A-C		not specified	Uncertain significance (Aug 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5DC3	protein_coding	protein_coding	ENST00000392876	14	70745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-7	0.990	125580	2	166	125748	0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	201	288	0.699	0.0000161	3609
Missense in Polyphen		86	139.23	0.61767		1602
Synonymous	1.63	86	108	0.800	0.00000638	991
Loss of Function	2.38	16	30.1	0.532	0.00000151	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000696	0.000695
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00108	0.00107
Middle Eastern	0.000109	0.000109
South Asian	0.000853	0.000817
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.848
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.194
• hipred: Y
• hipred_score: 0.639
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5dc3

Gene ontology

• Biological process: dephosphorylation
• Cellular component: receptor complex
• Molecular function: 5'-nucleotidase activity;metal ion binding