NMI

N-myc and STAT interactor

Basic information

Region (hg38): 2:151270470-151289894

Links

ENSG00000123609 ∙ NCBI:9111 ∙ OMIM:603525 ∙ HGNC:7854 ∙ Uniprot:Q13287 ∙ 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 NMI gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NMI 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			15	3		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in NMI

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

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

Position	Type	Phenotype	Significance	ClinVar
2-151270701-C-T		not specified	Uncertain significance (Mar 20, 2023)
2-151270705-G-T			not provided (-)
2-151270716-G-A		not specified	Likely benign (Dec 08, 2023)
2-151270725-C-G		not specified	Uncertain significance (Dec 19, 2023)
2-151270736-T-C		not specified	Uncertain significance (Nov 14, 2023)
2-151270875-T-A		not specified	Uncertain significance (May 14, 2024)
2-151271690-A-T		not specified	Uncertain significance (Oct 26, 2021)
2-151275486-C-G		not specified	Uncertain significance (Jun 27, 2023)
2-151275501-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-151275538-C-T		not specified	Uncertain significance (Jul 10, 2023)
2-151275541-G-A		not specified	Likely benign (Jun 22, 2021)
2-151275562-T-C		not specified	Uncertain significance (Aug 12, 2021)
2-151275564-C-T		not specified	Uncertain significance (Feb 27, 2023)
2-151275582-A-G		not specified	Uncertain significance (Apr 04, 2024)
2-151275638-A-T		not specified	Uncertain significance (Aug 28, 2023)
2-151275763-A-C		not specified	Uncertain significance (Mar 31, 2024)
2-151275840-C-T		not specified	Uncertain significance (Oct 03, 2022)
2-151275845-G-T		not specified	Likely benign (Jun 29, 2023)
2-151278915-T-C		not specified	Uncertain significance (Feb 16, 2023)
2-151278980-T-C		not specified	Uncertain significance (Jul 06, 2022)
2-151281962-T-C		not specified	Uncertain significance (Feb 28, 2023)
2-151282024-G-T		not specified	Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NMI	protein_coding	protein_coding	ENST00000243346	7	19593

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000870	0.779	125671	0	76	125747	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.127	163	159	1.03	0.00000802	2028
Missense in Polyphen		30	36.273	0.82707		510
Synonymous	0.365	53	56.5	0.938	0.00000306	536
Loss of Function	1.23	10	15.2	0.660	7.24e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000807	0.000807
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000112	0.000109
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000427	0.000422
Middle Eastern	0.000112	0.000109
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in augmenting coactivator protein recruitment to a group of sequence-specific transcription factors. Augments cytokine-mediated STAT transcription. Enhances CBP/p300 coactivator protein recruitment to STAT1 and STAT5.
• Pathway: IL-2 Signaling Pathway;il-7 signal transduction;il-2 receptor beta chain in t cell activation;IL2 (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.901
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.731
• hipred: N
• hipred_score: 0.352
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nmi

Gene ontology

• Biological process: transcription by RNA polymerase II;inflammatory response;JAK-STAT cascade;negative regulation of interferon-alpha biosynthetic process;negative regulation of interferon-beta biosynthetic process;negative regulation of innate immune response;interferon-gamma-mediated signaling pathway;positive regulation of protein K48-linked ubiquitination;regulation of nucleic acid-templated transcription
• Cellular component: nucleoplasm;cytoplasm;cytosol
• Molecular function: transcription coregulator activity;protein binding;identical protein binding