NOMO1

protein-coding

NODAL modulator 1

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 region of duplication located on the p 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 (PXE). [provided by RefSeq, Jul 2008]

MANE transcript

NM_014287.4

Inheritance

—

ClinVar variants

U:181B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr16:14,833,721-14,896,157

External References & Databases

Ensembl (ENSG00000103512)

Transcript & Mutation Effects

hg38 • Region Span ~62.4 kb

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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 NOMO1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 176

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014287.4. 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			3 clinvar	7 clinvar	1 clinvar	11
missense			170 clinvar	7 clinvar		177
nonsense						0
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	181	14	1	196

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014287.4	RefSeq	NP_055102.3	31	MANE Select
ENST00000287667.12	Ensembl	ENSP00000287667.7	31	MANE Select
ENST00000565655.1	Ensembl	ENSP00000457581.1	4	Standard
ENST00000880310.1	Ensembl	ENSP00000550369.1	31	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

endoplasmic reticulum membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000287667
Coding exons: 31
Length: 62480
Individuals with no LoFs: 125473
Homozygous LoFs: 0
Heterozygous LoFs: 117
Defined: 125590
p: 0.000466

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.517	454	486	0.934	0.0000287	7853
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00090	0.00086	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0021	0.0021	notable
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00053	0.00052	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.101

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.635

Gene Damage Prediction

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