MGARP
protein-codingmitochondria localized glutamic acid rich protein
Gene summary
Predicted to be involved in several processes, including axonal transport; negative regulation of dendrite development; and nervous system development. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]
- C4orf49
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.1 kbGenCC 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 MGARP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032623.4. 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 | 0 | |||||
| missense | 29 | 4 | 33 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 29 | 4 | 0 | 33 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_116012.2 | 4 | MANE Select | |
| Ensembl | ENSP00000381928.1 | 4 | MANE Select | |
| Ensembl | ENSP00000632498.1 | 4 | Standard | |
| Ensembl | ENSP00000632498.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein targeting to mitochondrion
- anterograde axonal transport
- retrograde axonal transport
- positive regulation of mitochondrion organization
- axonal transport of mitochondrion
Molecular Function
- protein binding
Cellular Component
- mitochondrion
- integral component of mitochondrial outer membrane
- axon cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000398955
- Coding exons
- 4
- Length
- 14176
- Individuals with no LoFs
- 124769
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 124781
- p
- 0.0000481
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.233 | 124 | 132 | 0.943 | 0.00000657 | 1526 |
| Missense (PolyPhen) | 29 | 29.135 | 0.99538 | 341 | ||
| Synonymous | -0.233 | 55 | 52.8 | 1.04 | 0.00000293 | 507 |
| Loss of Function | -0.508 | 6 | 4.80 | 1.25 | 2.00e-7 | 67 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000057 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000091 | 0.000079 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the trafficking of mitochondria along microtubules. Regulates the kinesin-mediated axonal transport of mitochondria to nerve terminals along microtubules during hypoxia. Participates in the translocation of TRAK2/GRIF1 from the cytoplasm to the mitochondrion. Also plays a role in steroidogenesis through maintenance of mitochondrial abundance and morphology (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0831
Intolerance Scores
- RVIS EVS
- 0.71
- RVIS percentile EVS
- 85.53
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |