NT5DC4

protein-coding

5'-nucleotidase domain containing 4

Gene summary

Predicted to enable 5'-nucleotidase activity. Predicted to be involved in GMP metabolic process and dGMP metabolic process. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001393655.1

Inheritance

—

ClinVar variants

B:1

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr2:112,721,020-112,742,879

External References & Databases

Ensembl (ENSG00000144130)

Transcript & Mutation Effects

hg38 • Region Span ~21.9 kb

Loading mutation effect viewer...

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 NT5DC4 variants in ClinVar

3 Conditions Cataloged

not providedTotal: 6

not specifiedTotal: 2

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393655.1. 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				1 clinvar		1
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	1	0	1

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393655.1	RefSeq	NP_001380584.1	17	MANE Select
ENST00000688554.1	Ensembl	ENSP00000509504.1	17	MANE Select
NM_001350494.2	RefSeq	NP_001337423.1	17	Standard
ENST00000327581.4	Ensembl	ENSP00000330247.4	17	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: ENST00000327581
Coding exons: 17
Length: 21394
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.616	213	240	0.888	0.0000132	2801
Missense (PolyPhen)		45	56.663	0.79417		835
Synonymous	1.11	80	93.6	0.854	0.00000533	780
Loss of Function	1.84	17	27.4	0.620	0.00000124	330

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0966

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0439

Gene Damage Prediction

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