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.

• not_specified (58 variants)
• not_provided (4 variants)

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. These statistics are base on transcript: NM_001004067.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			57	1		58
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	3	0

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