NT5C1A

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

Basic information

Region (hg38): 1:39651228-39672107

Links

ENSG00000116981 ∙ NCBI:84618 ∙ OMIM:610525 ∙ HGNC:17819 ∙ Uniprot:Q9BXI3 ∙ 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 NT5C1A gene.

• Inborn genetic diseases (12 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5C1A 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			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	3

Variants in NT5C1A

This is a list of pathogenic ClinVar variants found in the NT5C1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-39659132-A-C			Benign (Mar 02, 2018)
1-39659161-C-T		not specified	Uncertain significance (Jun 22, 2021)
1-39659401-C-T		not specified	Uncertain significance (Mar 11, 2022)
1-39659439-C-T			Benign (Jul 26, 2018)
1-39661099-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-39661117-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-39661152-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-39661162-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-39661178-G-A			Benign (Jul 10, 2017)
1-39661200-C-T		not specified	Uncertain significance (Aug 10, 2021)
1-39666133-A-C		not specified	Uncertain significance (Sep 01, 2021)
1-39666157-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-39666176-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-39666184-C-T		not specified	Uncertain significance (May 04, 2023)
1-39666199-G-A		not specified	Uncertain significance (Aug 20, 2023)
1-39671953-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-39672002-G-T		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5C1A	protein_coding	protein_coding	ENST00000235628	6	12918

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000834	0.934	125707	1	40	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.866	209	247	0.845	0.0000158	2397
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000599	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000158
Middle Eastern	0.000599	0.000598
South Asian	0.000197	0.000196
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Purine metabolism;adenosine nucleotides degradation;purine nucleotides degradation;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Pyrimidine metabolism;Purine catabolism (Consensus)

Recessive Scores

• pRec: 0.243

Intolerance Scores

• loftool: 0.241
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.421
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.156

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5c1a

Gene ontology

• Biological process: purine nucleotide catabolic process;nucleoside metabolic process;purine nucleoside monophosphate catabolic process;dephosphorylation;adenosine metabolic process;pyrimidine nucleoside catabolic process
• Cellular component: cytosol
• Molecular function: nucleotide binding;magnesium ion binding;protein binding;5'-nucleotidase activity