NDOR1

NADPH dependent diflavin oxidoreductase 1, the group of Cytosolic iron-sulfur assembly components

Basic information

Region (hg38): 9:137205685-137219361

Links

ENSG00000188566 ∙ NCBI:27158 ∙ OMIM:606073 ∙ HGNC:29838 ∙ Uniprot:Q9UHB4 ∙ 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 NDOR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDOR1 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			52	2		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	0

Variants in NDOR1

This is a list of pathogenic ClinVar variants found in the NDOR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137205788-C-T		not specified	Uncertain significance (Mar 31, 2024)
9-137205794-T-C		not specified	Uncertain significance (Jun 18, 2024)
9-137205800-T-A		not specified	Uncertain significance (Sep 25, 2024)
9-137205800-T-C		not specified	Uncertain significance (Feb 15, 2023)
9-137205823-A-G		not specified	Uncertain significance (Aug 13, 2021)
9-137205831-G-C		not specified	Uncertain significance (Mar 25, 2024)
9-137205842-A-G		not specified	Uncertain significance (Mar 12, 2024)
9-137205850-G-A		not specified	Uncertain significance (Dec 15, 2022)
9-137205907-C-T		not specified	Uncertain significance (Feb 13, 2023)
9-137206251-C-T		not specified	Uncertain significance (Jun 13, 2024)
9-137212523-C-T		not specified	Uncertain significance (Apr 24, 2023)
9-137212535-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-137212545-C-T		not specified	Uncertain significance (Jan 30, 2024)
9-137212586-T-G		not specified	Uncertain significance (Nov 04, 2022)
9-137212587-C-A		not specified	Uncertain significance (Nov 04, 2022)
9-137213790-G-A		not specified	Uncertain significance (Dec 20, 2023)
9-137213845-C-T		not specified	Uncertain significance (Jan 23, 2023)
9-137213978-C-T		not specified	Uncertain significance (Mar 20, 2023)
9-137213990-G-C		not specified	Uncertain significance (Oct 08, 2024)
9-137213996-G-C		not specified	Uncertain significance (Nov 16, 2021)
9-137214206-T-C		not specified	Uncertain significance (Feb 15, 2023)
9-137214262-G-A		not specified	Uncertain significance (Feb 13, 2024)
9-137214328-A-G		not specified	Uncertain significance (Mar 19, 2024)
9-137214339-C-G		not specified	Uncertain significance (Apr 12, 2022)
9-137214342-G-T		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDOR1	protein_coding	protein_coding	ENST00000371521	14	11315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.81e-13	0.328	125620	0	127	125747	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.614	422	388	1.09	0.0000256	3834
Missense in Polyphen		123	131.08	0.93838		1360
Synonymous	-1.16	187	168	1.11	0.0000106	1307
Loss of Function	1.20	23	30.1	0.764	0.00000154	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000452
Ashkenazi Jewish	0.00	0.00
East Asian	0.000926	0.000925
Finnish	0.00259	0.00236
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.000926	0.000925
South Asian	0.000458	0.000457
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cytosolic iron-sulfur (Fe-S) protein assembly (CIA) machinery. Required for the maturation of extramitochondrial Fe-S proteins (By similarity). Part of an electron transfer chain functioning in an early step of cytosolic Fe-S biogenesis. Transfers electrons from NADPH to the Fe/S cluster of CIAPIN1. {ECO:0000255|HAMAP-Rule:MF_03178, ECO:0000269|PubMed:10625700, ECO:0000269|PubMed:20802492, ECO:0000269|PubMed:23596212}.
• Pathway: Metabolism;Cytosolic iron-sulfur cluster assembly (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.0805
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.46

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.331
• ghis: 0.502

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndor1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; pigmentation phenotype; embryo phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: cell death;iron-sulfur cluster assembly;cellular response to menadione;oxidation-reduction process
• Cellular component: nucleus;cytoplasm;cytosol;intermediate filament cytoskeleton;perinuclear region of cytoplasm
• Molecular function: NADPH-hemoprotein reductase activity;protein binding;FMN binding;oxidoreductase activity;flavin adenine dinucleotide binding;NADP binding