NT5C1B-RDH14

NT5C1B-RDH14 readthrough

Basic information

Region (hg38): 2:18555545-18589564

Links

ENSG00000250741 ∙ NCBI:100526794 ∙ ∙ HGNC:38831 ∙ ∙ ∙ 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 NT5C1B-RDH14 gene.

• Inborn genetic diseases (47 variants)
• not provided (6 variants)
• Intellectual disability;Cerebellar atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5C1B-RDH14 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			33	3		36
nonsense					1	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	3	4

Highest pathogenic variant AF is 0.0000854353

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5C1B-RDH14	protein_coding	protein_coding	ENST00000532967	11	34020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.37e-10	0.881	112663	697	12388	125748	0.0535

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.250	364	378	0.964	0.0000243	3902
Missense in Polyphen		106	112.62	0.94123		1180
Synonymous	1.40	129	151	0.855	0.0000103	1188
Loss of Function	1.78	19	29.4	0.645	0.00000132	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.193	0.192
Ashkenazi Jewish	0.0272	0.0212
East Asian	0.0668	0.0601
Finnish	0.119	0.0669
European (Non-Finnish)	0.0503	0.0418
Middle Eastern	0.0668	0.0601
South Asian	0.0141	0.0121
Other	0.0505	0.0424

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity). {ECO:0000250}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Purine metabolism;adenosine nucleotides degradation;purine nucleotides degradation;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism;Purine catabolism (Consensus)

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 81.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.132
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: nucleotide metabolic process;dephosphorylation
• Cellular component: cytosol
• Molecular function: nucleotide binding;magnesium ion binding;5'-nucleotidase activity