IBA57
Basic information
Region (hg38): 1:228165804-228182257
Previous symbols: [ "C1orf69" ]
Links
Phenotypes
GenCC
Source:
- multiple mitochondrial dysfunctions syndrome 3 (Strong), mode of inheritance: AR
- multiple mitochondrial dysfunctions syndrome 3 (Supportive), mode of inheritance: AR
- hereditary spastic paraplegia 74 (Supportive), mode of inheritance: AR
- multiple mitochondrial dysfunctions syndrome 3 (Strong), mode of inheritance: AR
- hereditary spastic paraplegia 74 (Limited), mode of inheritance: AR
- mitochondrial disease (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Multiple mitochondrial dysfunctions syndrome 3; Spastic paraplegia 74, autosomal recessive | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Biochemical; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 23462291; 25609768 |
ClinVar
This is a list of variants' phenotypes submitted to
- Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 (7 variants)
- Multiple mitochondrial dysfunctions syndrome 3 (6 variants)
- Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 (3 variants)
- not provided (2 variants)
- Hereditary spastic paraplegia 74 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IBA57 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 | 64 | 67 | ||||
missense | 113 | 123 | ||||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 15 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
splice region | 1 | 2 | 2 | 1 | 6 | |
non coding | 12 | 17 | ||||
Total | 14 | 12 | 119 | 81 | 7 |
Highest pathogenic variant AF is 0.0000329
Variants in IBA57
This is a list of pathogenic ClinVar variants found in the IBA57 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-228165807-C-G | not specified | Uncertain significance (Sep 30, 2022) | ||
1-228165808-T-G | not specified | Likely benign (Oct 09, 2017) | ||
1-228165823-A-G | Inborn genetic diseases | Likely benign (Jan 10, 2022) | ||
1-228165827-C-T | Inborn genetic diseases • Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Uncertain significance (Jan 15, 2025) | ||
1-228165839-G-A | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 • Inborn genetic diseases | Uncertain significance (Jan 17, 2024) | ||
1-228165839-GA-G | Multiple mitochondrial dysfunctions syndrome 3 | Likely pathogenic (-) | ||
1-228165842-G-T | Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 | Uncertain significance (Sep 01, 2022) | ||
1-228165843-C-T | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Likely benign (Jan 06, 2025) | ||
1-228165844-G-A | Inborn genetic diseases | Uncertain significance (Aug 28, 2024) | ||
1-228165846-C-T | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Likely benign (Jun 05, 2023) | ||
1-228165847-A-T | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Uncertain significance (Dec 15, 2021) | ||
1-228165849-T-A | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Likely benign (Jul 25, 2023) | ||
1-228165855-G-A | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Likely benign (Sep 10, 2024) | ||
1-228165855-G-C | IBA57-related disorder | Likely benign (Nov 20, 2019) | ||
1-228165870-C-T | Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 | Likely benign (Sep 27, 2022) | ||
1-228165877-T-A | Inborn genetic diseases | Uncertain significance (Dec 21, 2023) | ||
1-228165884-TGC-T | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Pathogenic (May 21, 2022) | ||
1-228165893-C-T | Inborn genetic diseases | Uncertain significance (Nov 10, 2024) | ||
1-228165894-C-T | Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 | Likely benign (Mar 02, 2024) | ||
1-228165895-C-A | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Uncertain significance (Dec 03, 2021) | ||
1-228165898-A-G | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 • Inborn genetic diseases | Uncertain significance (Aug 27, 2024) | ||
1-228165900-G-A | Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 | Likely benign (Sep 08, 2023) | ||
1-228165901-T-G | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 | Uncertain significance (Oct 10, 2018) | ||
1-228165905-G-A | Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 • Inborn genetic diseases | Uncertain significance (Mar 09, 2022) | ||
1-228165910-G-A | Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 | Uncertain significance (Oct 17, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IBA57 | protein_coding | protein_coding | ENST00000366711 | 3 | 16443 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00839 | 0.939 | 125453 | 0 | 13 | 125466 | 0.0000518 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.572 | 219 | 196 | 1.11 | 0.0000124 | 2170 |
Missense in Polyphen | 62 | 65.768 | 0.94271 | 712 | ||
Synonymous | -1.83 | 115 | 92.6 | 1.24 | 0.00000587 | 827 |
Loss of Function | 1.67 | 5 | 11.0 | 0.455 | 8.00e-7 | 97 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000127 | 0.000123 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000166 | 0.000163 |
Finnish | 0.0000585 | 0.0000462 |
European (Non-Finnish) | 0.0000483 | 0.0000441 |
Middle Eastern | 0.000166 | 0.000163 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the maturation of mitochondrial 4Fe-4S proteins functioning late in the iron-sulfur cluster assembly pathway. {ECO:0000269|PubMed:23462291}.;
- Disease
- DISEASE: Spastic paraplegia 74, autosomal recessive (SPG74) [MIM:616451]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPG74 is characterized by a combination of spastic paraplegia, optic atrophy, and peripheral neuropathy with childhood-onset and slow progression into late adulthood. {ECO:0000269|PubMed:25609768}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0980
Haploinsufficiency Scores
- pHI
- 0.175
- hipred
- N
- hipred_score
- 0.233
- ghis
- 0.441
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Iba57
- Phenotype
Zebrafish Information Network
- Gene name
- iba57
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- heme biosynthetic process;iron-sulfur cluster assembly
- Cellular component
- mitochondrion;mitochondrial matrix
- Molecular function
- RNA binding;transferase activity