NT5C1B-RDH14

protein-coding

NT5C1B-RDH14 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring NT5C1B (5'-nucleotidase, cytosolic IB) and RDH14 (retinol dehydrogenase 14) genes on chromosome 2. Alternative splicing results in multiple transcript variants, one of which encodes a fusion protein that shares sequence identity with the products of each individual gene. [provided by RefSeq, Nov 2010]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:33B:7

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr2:18,555,545-18,589,564

External References & Databases

Ensembl (ENSG00000250741)

NCBI Gene (100526794)

HGNC:38831

GenCC

ClinVar (NT5C1B-RDH14)

Transcript & Mutation Effects

hg38 • Region Span ~34.0 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 NT5C1B-RDH14 variants in ClinVar

3 Conditions Cataloged

Inborn genetic diseasesTotal: 47

not providedTotal: 6

Intellectual disability;Cerebellar atrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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					3 clinvar	3
missense			33 clinvar	3 clinvar		36
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	3	4	40

Highest pathogenic variant AF is 0.0000854353

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001199103.2	RefSeq	NP_001186032.1	9	Standard
NM_001199104.2	RefSeq	NP_001186033.1	11	Standard
ENST00000444297.2	Ensembl	ENSP00000412639.2	9	Standard
ENST00000532967.5	Ensembl	ENSP00000433415.1	11	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)
Nucleobase catabolism
Metabolism of nucleotides

Biological Process

nucleotide metabolic process
dephosphorylation

Molecular Function

nucleotide binding
magnesium ion binding
5'-nucleotidase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000532967
Coding exons: 11
Length: 34020
Individuals with no LoFs: 112663
Homozygous LoFs: 697
Heterozygous LoFs: 12388
Defined: 125748
p: 0.0535

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.250	364	378	0.964	0.0000243	3902
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.025	0.024	notable
Latino/Admixed American	0.17	0.15	notable
Ashkenazi Jewish	0.027	0.021	notable
East Asian	0.067	0.060	notable
Finnish	0.12	0.067	notable
European (Non-Finnish)	0.050	0.042	notable
South Asian	0.014	0.012	notable
Other	0.050	0.042	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity). {ECO:0000250}.;

Intolerance Scores

RVIS EVS: 0.53
RVIS percentile EVS: 81.01

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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