IMMT

protein-coding

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

Gene summary

Enables RNA binding activity. Involved in cristae formation. Located in mitochondrial inner membrane. Part of MICOS complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006839.3

Inheritance

—

ClinVar variants

U:90B:12

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr2:86,143,932-86,195,472

External References & Databases

Ensembl (ENSG00000132305)

Transcript & Mutation Effects

hg38 • Region Span ~51.5 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 IMMT variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 15

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006839.3. 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	4 clinvar	4 clinvar	11
missense			84 clinvar	4 clinvar		88
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	90	8	4	102

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 169 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006839.3	RefSeq	NP_006830.2	15	MANE Select
ENST00000410111.8	Ensembl	ENSP00000387262.3	15	MANE Select
NM_001100169.2	RefSeq	NP_001093639.1	15	Standard
NM_001100170.2	RefSeq	NP_001093640.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cristae formation
mitochondrial calcium ion homeostasis

Molecular Function

RNA binding
protein binding

Cellular Component

mitochondrion
mitochondrial inner membrane
membrane
myelin sheath
MICOS complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000410111
Coding exons: 15
Length: 51839
Individuals with no LoFs: 124619
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 124639
p: 0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.763	350	393	0.892	0.0000211	4861
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00024	0.00022	rare
Finnish	0.000095	0.000093	rare
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.827

Gene Damage Prediction

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