NOMO2

NODAL modulator 2

Basic information

Region (hg38): 16:18417325-18562211

Links

ENSG00000185164 ∙ NCBI:283820 ∙ OMIM:609158 ∙ HGNC:22652 ∙ Uniprot:Q5JPE7 ∙ 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 NOMO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOMO2 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			53	2		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	53	2	0

Variants in NOMO2

This is a list of pathogenic ClinVar variants found in the NOMO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-18520609-C-T		not specified	Likely benign (Aug 12, 2021)
16-18520645-T-C		not specified	Uncertain significance (Feb 26, 2025)
16-18520766-G-A		not specified	Uncertain significance (Jan 23, 2023)
16-18520798-C-T		not specified	Uncertain significance (Jan 31, 2025)
16-18520816-A-G		not specified	Uncertain significance (Feb 26, 2025)
16-18520822-T-C		not specified	Uncertain significance (Mar 19, 2024)
16-18520865-C-T		not specified	Uncertain significance (Jul 31, 2024)
16-18520889-G-A		not specified	Uncertain significance (Jan 09, 2024)
16-18520889-G-C		not specified	Uncertain significance (Oct 01, 2024)
16-18520919-T-C		not specified	Uncertain significance (May 30, 2024)
16-18520921-C-T		not specified	Uncertain significance (Jan 23, 2025)
16-18520938-C-A		not specified	Uncertain significance (Aug 05, 2023)
16-18524515-A-T		not specified	Uncertain significance (Nov 23, 2024)
16-18524519-C-T		not specified	Uncertain significance (Nov 10, 2024)
16-18524520-G-A		not specified	Uncertain significance (Jun 18, 2021)
16-18524535-G-C		not specified	Uncertain significance (Dec 13, 2022)
16-18529563-C-A		not specified	Uncertain significance (Feb 15, 2023)
16-18529565-G-A		not specified	Uncertain significance (Dec 11, 2024)
16-18529598-C-A		not specified	Uncertain significance (Jun 02, 2023)
16-18531112-G-A		not specified	Uncertain significance (Mar 29, 2022)
16-18531114-T-C		not specified	Uncertain significance (Dec 14, 2023)
16-18531127-G-A		not specified	Uncertain significance (Jan 30, 2025)
16-18531142-G-C		not specified	Uncertain significance (Jun 21, 2021)
16-18531529-G-C		not specified	Uncertain significance (Jan 04, 2024)
16-18531532-T-C		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOMO2	protein_coding	protein_coding	ENST00000381474	32	62352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.97e-7	0.790	125553	1	37	125591	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	186	230	0.808	0.0000122	8148
Missense in Polyphen		35	54.466	0.64261		2061
Synonymous	1.04	82	94.8	0.865	0.00000571	2485
Loss of Function	1.34	12	18.1	0.661	8.52e-7	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000626	0.000626
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000159
Middle Eastern	0.00	0.00
South Asian	0.000133	0.0000980
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May antagonize Nodal signaling and subsequent organization of axial structures during mesodermal patterning, via its interaction with NCLN. {ECO:0000250}.

Recessive Scores

• pRec: 0.106

Haploinsufficiency Scores

• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Gene ontology

• Cellular component: endoplasmic reticulum membrane;integral component of membrane;protein-containing complex
• Molecular function: protein binding;carbohydrate binding