NT5C1A

protein-coding

5'-nucleotidase, cytosolic IA, the group of 5'-nucleotidases

Gene summary

Cytosolic nucleotidases, such as NT5C1A, dephosphorylate nucleoside monophosphates (Hunsucker et al., 2001 [PubMed 11133996]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_032526.3

Inheritance

—

ClinVar variants

U:47B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr1:39,651,229-39,672,107

External References & Databases

Ensembl (ENSG00000116981)

Transcript & Mutation Effects

hg38 • Region Span ~20.9 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 NT5C1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032526.3. 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			1 clinvar		2 clinvar	3
missense			45 clinvar	1 clinvar	1 clinvar	47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	47	1	3	51

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032526.3	RefSeq	NP_115915.1	6	MANE Select
ENST00000235628.2	Ensembl	ENSP00000235628.1	6	MANE Select
ENST00000905835.1	Ensembl	ENSP00000575894.1	6	Standard
ENST00000905835.2	Ensembl	ENSP00000575894.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyrimidine metabolism - Homo sapiens (human)
Nicotinate and nicotinamide metabolism - Homo sapiens (human)
Purine metabolism - Homo sapiens (human)
Pyrimidine catabolism
Nucleobase catabolism

Biological Process

purine nucleotide catabolic process
nucleoside metabolic process
purine nucleoside monophosphate catabolic process
dephosphorylation
adenosine metabolic process

Molecular Function

nucleotide binding
magnesium ion binding
protein binding
5'-nucleotidase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000235628
Coding exons: 6
Length: 12918
Individuals with no LoFs: 125707
Homozygous LoFs: 1
Heterozygous LoFs: 40
Defined: 125748
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.866	209	247	0.845	0.0000158	2397
Missense (PolyPhen)		68	101.59	0.66934		966
Synonymous	-0.0874	104	103	1.01	0.00000701	750
Loss of Function	1.68	9	16.3	0.552	9.49e-7	170

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia. {ECO:0000269|PubMed:11133996}.;

Recessive Scores

pRec: 0.243

Intolerance Scores

LoFtool: 0.241
RVIS EVS: -0.23
RVIS percentile EVS: 37.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.156

Gene Damage Prediction

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