IMMT

inner membrane mitochondrial protein, the group of MicroRNA protein coding host genes|Mitochondrial contact site and cristae organizing system subunits

Basic information

Region (hg38): 2:86143932-86195472

Links

ENSG00000132305 ∙ NCBI:10989 ∙ OMIM:600378 ∙ HGNC:6047 ∙ Uniprot:Q16891 ∙ 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 IMMT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMMT 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				3	4	7
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	6	4

Variants in IMMT

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

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

Position	Type	Phenotype	Significance	ClinVar
2-86144303-C-A		not specified	Uncertain significance (Oct 12, 2022)
2-86144303-C-T		not specified	Uncertain significance (Aug 03, 2022)
2-86144334-T-C		not specified	Uncertain significance (Mar 29, 2024)
2-86144389-C-T		not specified	Uncertain significance (Jan 06, 2023)
2-86144434-T-C		not specified	Uncertain significance (Oct 01, 2024)
2-86144449-T-G		not specified	Uncertain significance (Nov 07, 2022)
2-86144494-T-C		not specified	Uncertain significance (Apr 23, 2024)
2-86144518-G-A		not specified	Uncertain significance (Dec 04, 2024)
2-86144525-G-A			Benign (Dec 31, 2019)
2-86144572-T-C		not specified	Uncertain significance (Oct 09, 2024)
2-86144645-G-C		not specified	Uncertain significance (Jun 22, 2023)
2-86144646-G-A			Likely benign (Jun 26, 2018)
2-86144648-C-A		not specified	Uncertain significance (Sep 25, 2024)
2-86144705-C-T			Likely benign (Oct 24, 2018)
2-86144709-T-A		not specified	Uncertain significance (May 04, 2022)
2-86144714-C-T		not specified	Uncertain significance (Oct 03, 2022)
2-86144737-C-A		not specified	Uncertain significance (Feb 28, 2024)
2-86144743-G-A		not specified	Likely benign (Oct 07, 2024)
2-86144764-C-G		not specified	Uncertain significance (Oct 16, 2023)
2-86144828-C-G		not specified	Uncertain significance (Feb 05, 2024)
2-86146107-C-T		not specified	Uncertain significance (Dec 15, 2022)
2-86146155-G-A		not specified	Uncertain significance (Jul 20, 2021)
2-86147735-T-A			Likely benign (Jul 17, 2018)
2-86147781-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-86147808-T-G		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IMMT	protein_coding	protein_coding	ENST00000410111	15	51839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0133	0.987	124619	0	20	124639	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.763	350	393	0.892	0.0000211	4861
Missense in Polyphen		98	122.63	0.79916		1465
Synonymous	0.348	142	147	0.964	0.00000782	1511
Loss of Function	4.11	11	38.5	0.285	0.00000220	471

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000238	0.000223
Finnish	0.0000954	0.0000928
European (Non-Finnish)	0.0000455	0.0000442
Middle Eastern	0.000238	0.000223
South Asian	0.000166	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology (PubMed:22114354, PubMed:25781180). {ECO:0000269|PubMed:22114354, ECO:0000269|PubMed:25781180}.

Recessive Scores

• pRec: 0.387

Intolerance Scores

• loftool: 0.660
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.489
• hipred: Y
• hipred_score: 0.542
• ghis: 0.597

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.827

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Immt

Gene ontology

• Biological process: cristae formation;mitochondrial calcium ion homeostasis
• Cellular component: mitochondrion;mitochondrial inner membrane;membrane;myelin sheath;MICOS complex
• Molecular function: RNA binding;protein binding