NUDT6

protein-coding

nudix hydrolase 6, the group of Nudix hydrolase family

Gene summary

This gene overlaps and lies on the opposite strand from FGF2 gene, and is thought to be the FGF2 antisense gene. The two genes are independently transcribed, and their expression shows an inverse relationship, suggesting that this antisense transcript may regulate FGF2 expression. This gene has also been shown to have hormone-regulatory and antiproliferative actions in the pituitary that are independent of FGF2 expression. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_007083.5

Inheritance

—

ClinVar variants

U:44B:8

Top phenotype

NUDT6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr4:122,888,697-122,922,968

External References & Databases

Ensembl (ENSG00000170917)

Transcript & Mutation Effects

hg38 • Region Span ~34.3 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 NUDT6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

NUDT6-related disorderTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007083.5. 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				4 clinvar		4
missense			42 clinvar	2 clinvar	2 clinvar	46
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	44	6	2	52

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007083.5	RefSeq	NP_009014.2	5	MANE Select
ENST00000304430.10	Ensembl	ENSP00000306070.5	5	MANE Select
NM_198041.3	RefSeq	NP_932158.1	2	Standard
ENST00000339154.6	Ensembl	ENSP00000344011.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cell population proliferation
negative regulation of cell cycle

Molecular Function

NADH pyrophosphatase activity
ADP-ribose diphosphatase activity
NAD binding

Cellular Component

nucleus
cytoplasm
mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304430
Coding exons: 5
Length: 34272
Individuals with no LoFs: 125569
Homozygous LoFs: 0
Heterozygous LoFs: 179
Defined: 125748
p: 0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0242	175	174	1.01	0.00000852	1991
Missense (PolyPhen)		70	74.543	0.93905		932
Synonymous	-0.765	82	73.6	1.11	0.00000380	652
Loss of Function	1.73	10	17.9	0.559	0.00000107	171

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.0013	0.0013	notable
South Asian	0.00023	0.00023	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May contribute to the regulation of cell proliferation. {ECO:0000269|PubMed:11266510}.;

Recessive Scores

pRec: 0.256

Intolerance Scores

LoFtool: 0.784
RVIS EVS: 0.64
RVIS percentile EVS: 83.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.194

Gene Damage Prediction

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