NOMO1

NODAL modulator 1

Basic information

Region (hg38): 16:14833721-14896157

Links

ENSG00000103512 ∙ NCBI:23420 ∙ OMIM:609157 ∙ HGNC:30060 ∙ Uniprot:Q15155 ∙ 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 NOMO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOMO1 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				2	1	3
missense			94	4		98
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding						0
Total	0	0	94	6	1

Variants in NOMO1

This is a list of pathogenic ClinVar variants found in the NOMO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-14833859-T-G		not specified	Uncertain significance (Jul 06, 2021)
16-14833865-A-G		not specified	Likely benign (Jun 17, 2022)
16-14838419-A-G		not specified	Uncertain significance (Sep 27, 2021)
16-14838461-A-G		not specified	Uncertain significance (May 04, 2022)
16-14844671-C-T			Likely benign (Feb 01, 2023)
16-14846618-G-C		not specified	Uncertain significance (Mar 29, 2022)
16-14846643-G-A		not specified	Uncertain significance (May 05, 2023)
16-14852457-T-C		not specified	Uncertain significance (Jan 31, 2023)
16-14852463-G-A		not specified	Uncertain significance (May 13, 2024)
16-14852478-C-T		not specified	Uncertain significance (Dec 13, 2022)
16-14852521-G-A		not specified	Uncertain significance (Jun 07, 2024)
16-14853543-C-T		not specified	Uncertain significance (Jan 20, 2023)
16-14853564-C-T		not specified	Uncertain significance (Feb 14, 2025)
16-14853947-A-G		not specified	Uncertain significance (Aug 01, 2024)
16-14853961-A-T		not specified	Uncertain significance (Apr 18, 2023)
16-14853988-C-T		not specified	Uncertain significance (Oct 21, 2024)
16-14854024-G-A		not specified	Uncertain significance (Jan 10, 2022)
16-14854025-A-G		not specified	Uncertain significance (May 25, 2022)
16-14857220-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-14857229-G-A		not specified	Uncertain significance (Nov 10, 2024)
16-14857244-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-14857264-C-T			Likely benign (Feb 26, 2018)
16-14857566-C-G		not specified	Uncertain significance (Nov 15, 2021)
16-14857571-C-T		not specified	Uncertain significance (Mar 28, 2024)
16-14857598-C-T		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOMO1	protein_coding	protein_coding	ENST00000287667	31	62480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-19	0.149	125473	0	117	125590	0.000466

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.517	454	486	0.934	0.0000287	7853
Missense in Polyphen		112	133.14	0.84122		2079
Synonymous	-1.19	224	203	1.11	0.0000137	2393
Loss of Function	1.43	35	45.4	0.771	0.00000216	768

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00134	0.00130
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00207	0.00207
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000212	0.000212
Middle Eastern	0.00207	0.00207
South Asian	0.000531	0.000523
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.101

Haploinsufficiency Scores

• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.635

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nomo1

Gene ontology

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