IBA57

iron-sulfur cluster assembly factor IBA57, the group of Mitochondrial iron-sulfur assembly components

Basic information

Region (hg38): 1:228165804-228182257

Previous symbols: [ "C1orf69" ]

Links

ENSG00000181873NCBI:200205OMIM:615316HGNC:27302Uniprot:Q5T440AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Multiple mitochondrial dysfunctions syndrome 3; Spastic paraplegia 74, autosomal recessiveARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic23462291; 25609768

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IBA57 gene.

  • 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
2
clinvar
64
clinvar
1
clinvar
67
missense
1
clinvar
2
clinvar
113
clinvar
5
clinvar
2
clinvar
123
nonsense
7
clinvar
7
start loss
0
frameshift
6
clinvar
6
clinvar
3
clinvar
15
inframe indel
0
splice donor/acceptor (+/-2bp)
4
clinvar
4
splice region
1
2
2
1
6
non coding
1
clinvar
12
clinvar
4
clinvar
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)1722361
1-228165808-T-G not specified Likely benign (Oct 09, 2017)512242
1-228165823-A-G Inborn genetic diseases Likely benign (Jan 10, 2022)2402894
1-228165827-C-T Inborn genetic diseases • Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Uncertain significance (Jan 15, 2025)651713
1-228165839-G-A Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 • Inborn genetic diseases Uncertain significance (Jan 17, 2024)1507732
1-228165839-GA-G Multiple mitochondrial dysfunctions syndrome 3 Likely pathogenic (-)2585593
1-228165842-G-T Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 Uncertain significance (Sep 01, 2022)1936924
1-228165843-C-T Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Likely benign (Jan 06, 2025)1879115
1-228165844-G-A Inborn genetic diseases Uncertain significance (Aug 28, 2024)3527345
1-228165846-C-T Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Likely benign (Jun 05, 2023)2935584
1-228165847-A-T Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Uncertain significance (Dec 15, 2021)1410916
1-228165849-T-A Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Likely benign (Jul 25, 2023)2921790
1-228165855-G-A Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Likely benign (Sep 10, 2024)2953023
1-228165855-G-C IBA57-related disorder Likely benign (Nov 20, 2019)3053335
1-228165870-C-T Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 Likely benign (Sep 27, 2022)2193856
1-228165877-T-A Inborn genetic diseases Uncertain significance (Dec 21, 2023)3107845
1-228165884-TGC-T Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Pathogenic (May 21, 2022)1997279
1-228165893-C-T Inborn genetic diseases Uncertain significance (Nov 10, 2024)3527344
1-228165894-C-T Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 Likely benign (Mar 02, 2024)3753161
1-228165895-C-A Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Uncertain significance (Dec 03, 2021)2017506
1-228165898-A-G Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 • Inborn genetic diseases Uncertain significance (Aug 27, 2024)1946523
1-228165900-G-A Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 Likely benign (Sep 08, 2023)2953199
1-228165901-T-G Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 Uncertain significance (Oct 10, 2018)662694
1-228165905-G-A Multiple mitochondrial dysfunctions syndrome 3;Hereditary spastic paraplegia 74 • Inborn genetic diseases Uncertain significance (Mar 09, 2022)1512645
1-228165910-G-A Hereditary spastic paraplegia 74;Multiple mitochondrial dysfunctions syndrome 3 Uncertain significance (Oct 17, 2022)2074055

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IBA57protein_codingprotein_codingENST00000366711 316443
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.008390.9391254530131254660.0000518
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5722191961.110.00001242170
Missense in Polyphen6265.7680.94271712
Synonymous-1.8311592.61.240.00000587827
Loss of Function1.67511.00.4558.00e-797

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001270.000123
Ashkenazi Jewish0.000.00
East Asian0.0001660.000163
Finnish0.00005850.0000462
European (Non-Finnish)0.00004830.0000441
Middle Eastern0.0001660.000163
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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