NT5DC2

protein-coding

5'-nucleotidase domain containing 2

Gene summary

Predicted to enable 5'-nucleotidase activity. Predicted to be involved in negative regulation of dopamine biosynthetic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001134231.2

Inheritance

—

ClinVar variants

U:124B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr3:52,524,385-52,535,054

External References & Databases

Ensembl (ENSG00000168268)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NT5DC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001134231.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			111 clinvar			111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	124	2	0	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 48 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001134231.2	RefSeq	NP_001127703.1	14	MANE Select
ENST00000422318.7	Ensembl	ENSP00000406933.2	14	MANE Select
NM_022908.3	RefSeq	NP_075059.1	14	Standard
ENST00000307076.8	Ensembl	ENSP00000302468.4	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

dephosphorylation

Molecular Function

5'-nucleotidase activity
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000422318
Coding exons: 14
Length: 10685
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125701
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.04	274	327	0.838	0.0000229	3623
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00049	0.00049	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00026	0.00024	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0995

Intolerance Scores

LoFtool: 0.699
RVIS EVS: -0.8
RVIS percentile EVS: 12.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.669

Gene Damage Prediction

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