NOM1

protein-coding

nucleolar protein with MIF4G domain 1, the group of MIF4G domain containing proteins|SSU processome|Protein phosphatase 1 regulatory subunits

Gene summary

Proteins that contain MIF4G (middle of eIF4G (MIM 600495)) and/or MA3 domains, such as NOM1, function in protein translation. These domains include binding sites for members of the EIF4A family of ATP-dependent DEAD box RNA helicases (see EIF4A1; MIM 602641) (Simmons et al., 2005 [PubMed 15715967]).[supplied by OMIM, Mar 2008]

Previous symbols:

C7orf3

MANE transcript

NM_138400.2

Inheritance

—

ClinVar variants

U:179B:9

Top phenotype

NOM1-related condition

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr7:156,949,712-156,973,176

External References & Databases

Ensembl (ENSG00000146909)

Transcript & Mutation Effects

hg38 • Region Span ~23.5 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 NOM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 178

NOM1-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138400.2. 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			174 clinvar	9 clinvar		183
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	179	9	0	188

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138400.2	RefSeq	NP_612409.1	11	MANE Select
ENST00000275820.4	Ensembl	ENSP00000275820.3	11	MANE Select
NM_001353366.2	RefSeq	NP_001340295.1	11	Standard
ENST00000851672.1	Ensembl	ENSP00000521731.1	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nom1	Danio rerio	Structure: intestine Quality: decreased thickness abnormal

Gene / Model

Organism

Observed Phenotype

nom1

Danio rerio

Structure: intestine

Quality: decreased thickness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
ribosomal small subunit biogenesis
hair follicle maturation

Molecular Function

RNA binding
protein binding

Cellular Component

nucleus
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000275820
Coding exons: 11
Length: 23460
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.966	550	490	1.12	0.0000262	5610
Missense (PolyPhen)		136	126.27	1.0771		1577
Synonymous	0.0389	201	202	0.997	0.0000122	1647
Loss of Function	1.99	20	32.2	0.622	0.00000147	422

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00054	0.00054	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00034	0.00029	rare
South Asian	0.000066	0.000065	rare
Other	0.00065	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in targeting PPP1CA to the nucleolus. {ECO:0000269|PubMed:17965019}.;

Intolerance Scores

LoFtool: 0.863
RVIS EVS: 1.16
RVIS percentile EVS: 92.65

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.962

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High