NT5DC3

protein-coding

5'-nucleotidase domain containing 3

Gene summary

Predicted to enable 5'-nucleotidase activity. Located in mitochondrion. Part of signaling receptor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001031701.3

Inheritance

—

ClinVar variants

U:60B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr12:103,770,453-103,841,234

External References & Databases

Ensembl (ENSG00000111696)

Transcript & Mutation Effects

hg38 • Region Span ~70.8 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 NT5DC3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031701.3. 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						0
missense			58 clinvar	3 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	3	0	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031701.3	RefSeq	NP_001026871.1	14	MANE Select
ENST00000392876.8	Ensembl	ENSP00000376615.3	14	MANE Select
ENST00000415849.1	Ensembl	ENSP00000399171.1	5	Standard
ENST00000447799.5	Ensembl	ENSP00000413657.1	3	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

Cellular Component

receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392876
Coding exons: 14
Length: 70745
Individuals with no LoFs: 125580
Homozygous LoFs: 2
Heterozygous LoFs: 166
Defined: 125748
p: 0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.82	201	288	0.699	0.0000161	3609
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00020	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.00085	0.00082	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.848
RVIS EVS: -0.56
RVIS percentile EVS: 19.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.278

Gene Damage Prediction

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