OXNAD1

oxidoreductase NAD binding domain containing 1

Basic information

Region (hg38): 3:16265159-16350299

Links

ENSG00000154814 ∙ NCBI:92106 ∙ ∙ HGNC:25128 ∙ Uniprot:Q96HP4 ∙ 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 OXNAD1 gene.

• Inborn genetic diseases (25 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXNAD1 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						0
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	2		12
Total	0	0	24	3	0

Variants in OXNAD1

This is a list of pathogenic ClinVar variants found in the OXNAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-16270989-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-16271004-G-A		not specified	Uncertain significance (Jun 26, 2023)
3-16271023-C-T		not specified	Uncertain significance (Oct 06, 2021)
3-16271035-T-G		not specified	Uncertain significance (Dec 16, 2023)
3-16271673-A-G		not specified	Uncertain significance (May 31, 2023)
3-16271709-T-G		not specified	Uncertain significance (Mar 07, 2024)
3-16271717-C-T		not specified	Uncertain significance (Dec 18, 2023)
3-16286342-A-G		not specified	Likely benign (Oct 06, 2022)
3-16294937-A-T		not specified	Uncertain significance (Mar 29, 2022)
3-16294978-C-T		not specified	Uncertain significance (May 17, 2023)
3-16301692-G-A		not specified	Uncertain significance (Jun 29, 2022)
3-16301726-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-16301800-A-G		not specified	Uncertain significance (Nov 15, 2021)
3-16301827-C-G		not specified	Uncertain significance (Oct 27, 2022)
3-16301856-A-T		not specified	Uncertain significance (Dec 13, 2021)
3-16302650-T-G		not specified	Uncertain significance (Oct 02, 2023)
3-16302680-T-C		not specified	Uncertain significance (Jan 23, 2023)
3-16302683-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-16303465-A-G		not specified	Uncertain significance (Nov 22, 2022)
3-16303467-A-C		not specified	Uncertain significance (Oct 06, 2023)
3-16303521-C-T		not specified	Uncertain significance (Oct 20, 2021)
3-16316835-T-C		not specified	Uncertain significance (Aug 18, 2021)
3-16316844-G-A		not specified	Uncertain significance (Nov 09, 2021)
3-16316999-A-G			Likely benign (Mar 01, 2023)
3-16317041-C-T		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXNAD1	protein_coding	protein_coding	ENST00000285083	7	85101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.42e-8	0.216	125570	0	177	125747	0.000704

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.454	189	172	1.10	0.00000901	2027
Missense in Polyphen		35	39.914	0.87688		488
Synonymous	1.00	52	62.0	0.838	0.00000326	615
Loss of Function	0.325	12	13.3	0.904	6.19e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000628	0.000627
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.000220	0.000217
South Asian	0.00384	0.00383
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0848

Intolerance Scores

• loftool: 0.589
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.0250
• hipred: N
• hipred_score: 0.197
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oxnad1

Gene ontology

• Biological process: biological_process;oxidation-reduction process
• Cellular component: cellular_component
• Molecular function: molecular_function;oxidoreductase activity