NOMO3

NODAL modulator 3

Basic information

Region (hg38): 16:16232506-16300806

Links

ENSG00000103226 ∙ NCBI:408050 ∙ OMIM:609159 ∙ HGNC:25242 ∙ Uniprot:P69849 ∙ 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 NOMO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOMO3 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				1		1
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in NOMO3

This is a list of pathogenic ClinVar variants found in the NOMO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-16232671-T-G		not specified	Likely benign (Oct 13, 2021)
16-16232673-G-C		not specified	Uncertain significance (Nov 03, 2023)
16-16232676-G-C		not specified	Uncertain significance (Feb 17, 2024)
16-16232676-G-T		not specified	Uncertain significance (Jul 16, 2024)
16-16232681-G-C		not specified	Uncertain significance (May 24, 2023)
16-16232713-C-T		not specified	Uncertain significance (Nov 18, 2022)
16-16232766-G-A		not specified	Uncertain significance (Oct 12, 2021)
16-16236945-C-G		not specified	Uncertain significance (May 29, 2024)
16-16243165-G-A			Likely benign (Mar 01, 2022)
16-16245129-G-A		not specified	Uncertain significance (Feb 13, 2024)
16-16251016-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-16251042-G-A		not specified	Uncertain significance (Jan 23, 2025)
16-16251957-G-A			Uncertain significance (Mar 01, 2025)
16-16255763-T-C		not specified	Uncertain significance (Mar 20, 2023)
16-16255805-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-16255815-C-G		not specified	Uncertain significance (Feb 07, 2025)
16-16256008-T-A		not specified	Uncertain significance (Oct 28, 2024)
16-16256008-T-C		not specified	Uncertain significance (Feb 15, 2023)
16-16256073-G-C		not specified	Uncertain significance (Aug 16, 2022)
16-16261533-C-T		not specified	Uncertain significance (May 08, 2024)
16-16261578-C-A		not specified	Uncertain significance (Sep 26, 2022)
16-16261587-C-G		not specified	Uncertain significance (Apr 15, 2024)
16-16261592-C-G		not specified	Uncertain significance (Dec 30, 2024)
16-16261614-G-A		not specified	Uncertain significance (May 25, 2022)
16-16261629-C-T		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOMO3	protein_coding	protein_coding	ENST00000399336	31	62317

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000958	0.987	123818	4	36	123858	0.000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	174	220	0.789	0.0000122	7907
Missense in Polyphen		49	70.056	0.69944		2540
Synonymous	0.771	78	87.2	0.895	0.00000542	2428
Loss of Function	2.21	10	20.9	0.478	9.79e-7	772

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000732	0.000609
Ashkenazi Jewish	0.00	0.00
East Asian	0.000383	0.000353
Finnish	0.00	0.00
European (Non-Finnish)	0.000164	0.000150
Middle Eastern	0.000383	0.000353
South Asian	0.000236	0.000198
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May antagonize Nodal signaling. {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Haploinsufficiency Scores

• pHI: 0.266
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.691

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: molecular_function;carbohydrate binding