NT5DC2

5'-nucleotidase domain containing 2

Basic information

Region (hg38): 3:52524384-52535054

Links

ENSG00000168268 ∙ NCBI:64943 ∙ ∙ HGNC:25717 ∙ Uniprot:Q9H857 ∙ 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 NT5DC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5DC2 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			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	38	2	0

Variants in NT5DC2

This is a list of pathogenic ClinVar variants found in the NT5DC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52524475-G-A		not specified	Uncertain significance (May 23, 2024)
3-52524517-C-T		not specified	Uncertain significance (Oct 06, 2022)
3-52524561-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-52524594-C-T		not specified	Uncertain significance (Jul 22, 2022)
3-52524830-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-52524838-A-T		not specified	Uncertain significance (Nov 18, 2022)
3-52524854-C-A		not specified	Uncertain significance (Feb 07, 2023)
3-52524994-T-G		not specified	Uncertain significance (Apr 22, 2024)
3-52525048-C-T		not specified	Uncertain significance (Nov 14, 2023)
3-52525062-G-C		not specified	Uncertain significance (Nov 28, 2023)
3-52525069-G-A		not specified	Uncertain significance (Aug 02, 2021)
3-52525070-C-T		not specified	Uncertain significance (Apr 30, 2024)
3-52525085-C-A		not specified	Uncertain significance (Jun 16, 2023)
3-52525097-T-A		not specified	Uncertain significance (Dec 13, 2022)
3-52525247-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-52525250-G-A		not specified	Uncertain significance (Oct 24, 2023)
3-52525259-G-A		not specified	Uncertain significance (Sep 26, 2022)
3-52525274-G-A		not specified	Uncertain significance (Jun 22, 2023)
3-52527332-G-A		not specified	Uncertain significance (May 31, 2023)
3-52527681-G-A		not specified	Uncertain significance (May 16, 2022)
3-52527699-T-C		not specified	Uncertain significance (Jan 17, 2024)
3-52528038-C-T		not specified	Uncertain significance (Oct 07, 2022)
3-52528229-C-G		not specified	Uncertain significance (Nov 15, 2021)
3-52528276-C-T			Likely benign (Mar 01, 2022)
3-52528638-T-C		not specified	Uncertain significance (Jun 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5DC2	protein_coding	protein_coding	ENST00000422318	14	10685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000121	0.998	125643	0	58	125701	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	274	327	0.838	0.0000229	3623
Missense in Polyphen		148	165.99	0.89162		1660
Synonymous	-0.866	141	129	1.10	0.00000922	1079
Loss of Function	2.70	13	28.6	0.454	0.00000132	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000266	0.000265
Ashkenazi Jewish	0.000303	0.000298
East Asian	0.000490	0.000489
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000258	0.000238
Middle Eastern	0.000490	0.000489
South Asian	0.000164	0.000163
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0995

Intolerance Scores

• loftool: 0.699
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.487
• hipred: N
• hipred_score: 0.423
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.669

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5dc2

Gene ontology

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