NOM1

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

Basic information

Region (hg38): 7:156949712-156973176

Previous symbols: [ "C7orf3" ]

Links

ENSG00000146909 ∙ NCBI:64434 ∙ OMIM:611269 ∙ HGNC:13244 ∙ Uniprot:Q5C9Z4 ∙ 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 NOM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOM1 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			68	3		71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	3	0

Variants in NOM1

This is a list of pathogenic ClinVar variants found in the NOM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-156949742-C-T		not specified	Uncertain significance (May 09, 2023)
7-156949771-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-156949798-C-A		not specified	Uncertain significance (Aug 30, 2021)
7-156949819-C-A		not specified	Uncertain significance (Nov 12, 2021)
7-156949831-C-T		not specified	Uncertain significance (Nov 22, 2023)
7-156949888-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-156949901-C-T		not specified	Uncertain significance (May 30, 2022)
7-156949932-C-G		not specified	Uncertain significance (Nov 21, 2023)
7-156949942-G-C		not specified	Uncertain significance (Sep 26, 2023)
7-156949945-G-A		not specified	Uncertain significance (Nov 07, 2022)
7-156949967-G-A		not specified	Uncertain significance (Mar 15, 2024)
7-156949981-C-T		not specified	Uncertain significance (Nov 09, 2023)
7-156949982-G-C		not specified	Uncertain significance (Mar 31, 2024)
7-156950048-C-G		not specified	Uncertain significance (Jan 08, 2024)
7-156950066-T-C		not specified	Likely benign (Jul 06, 2022)
7-156950089-G-A		not specified	Uncertain significance (Sep 26, 2022)
7-156950110-G-A		not specified	Uncertain significance (Sep 27, 2022)
7-156950114-C-T		not specified	Uncertain significance (Apr 07, 2023)
7-156950143-C-G		not specified	Uncertain significance (Jul 31, 2023)
7-156950174-C-A		not specified	Uncertain significance (Dec 11, 2023)
7-156950216-C-A		not specified	Uncertain significance (Feb 22, 2023)
7-156950239-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-156950245-G-A		not specified	Uncertain significance (Nov 18, 2022)
7-156950272-A-G		not specified	Uncertain significance (Aug 10, 2021)
7-156950326-A-C		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOM1	protein_coding	protein_coding	ENST00000275820	11	23460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.19e-10	0.937	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.966	550	490	1.12	0.0000262	5610
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000630	0.000626
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000544	0.000544
Finnish	0.000281	0.000277
European (Non-Finnish)	0.000338	0.000290
Middle Eastern	0.000544	0.000544
South Asian	0.0000655	0.0000653
Other	0.000652	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0857
• hipred: Y
• hipred_score: 0.553
• ghis: 0.467

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nom1

Zebrafish Information Network

• Gene name: nom1
• Affected structure: intestine
• Phenotype tag: abnormal
• Phenotype quality: decreased thickness

Gene ontology

• Biological process: biological_process;ribosomal small subunit biogenesis;hair follicle maturation
• Cellular component: nucleus;nucleolus
• Molecular function: RNA binding;protein binding