NOMO3

protein-coding

NODAL modulator 3

Gene summary

This gene encodes a protein originally thought to be related to the collagenase gene family. This gene is one of three highly similar genes in a duplicated region on the short arm of chromosome 16. These three genes encode closely related proteins that may have the same function. The protein encoded by one of these genes has been identified as part of a protein complex that participates in the Nodal signaling pathway during vertebrate development. Mutations in ABCC6, which is located nearby, rather than mutations in this gene are associated with pseudoxanthoma elasticum. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001004067.4

Inheritance

—

ClinVar variants

U:72B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr16:16,232,506-16,300,806

External References & Databases

Ensembl (ENSG00000103226)

Transcript & Mutation Effects

hg38 • Region Span ~68.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NOMO3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004067.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			69 clinvar	2 clinvar		71
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	72	4	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001004067.4	RefSeq	NP_001004067.1	31	MANE Select
ENST00000399336.9	Ensembl	ENSP00000382274.4	31	MANE Select
ENST00000263012.10	Ensembl	ENSP00000263012.6	32	Standard
ENST00000263012.11	Ensembl	ENSP00000263012.6	32	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function
carbohydrate binding

Cellular Component

cellular_component
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399336
Coding exons: 31
Length: 62317
Individuals with no LoFs: 123818
Homozygous LoFs: 4
Heterozygous LoFs: 36
Defined: 123858
p: 0.000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.11	174	220	0.789	0.0000122	7907
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00059	0.00046	rare
Latino/Admixed American	0.00015	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00035	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.00024	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.102

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.691

Gene Damage Prediction

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