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NM_030940.4(ISCA1):c.259G>A (p.Glu87Lys) AND Multiple mitochondrial dysfunctions syndrome 5

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Mar 14, 2023
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000497255.10

Allele description [Variation Report for NM_030940.4(ISCA1):c.259G>A (p.Glu87Lys)]

NM_030940.4(ISCA1):c.259G>A (p.Glu87Lys)

Gene:
ISCA1:iron-sulfur cluster assembly 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q21.33
Genomic location:
Preferred name:
NM_030940.4(ISCA1):c.259G>A (p.Glu87Lys)
HGVS:
  • NC_000009.12:g.86266174C>T
  • NM_030940.4:c.259G>AMANE SELECT
  • NP_112202.2:p.Glu87Lys
  • NC_000009.11:g.88881089C>T
  • NM_030940.3:c.259G>A
Protein change:
E87K; GLU87LYS
Links:
OMIM: 611006.0001; dbSNP: rs776679653
NCBI 1000 Genomes Browser:
rs776679653
Molecular consequence:
  • NM_030940.4:c.259G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Multiple mitochondrial dysfunctions syndrome 5
Identifiers:
MONDO: MONDO:0033282; MedGen: C4539919; OMIM: 617613

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000588867OMIM
no assertion criteria provided
Pathogenic
(Jul 8, 2020)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000999924GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV001963618Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenicinheritedclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004235809Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 14, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedinheritedyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Homozygous p.(Glu87Lys) variant in ISCA1 is associated with a multiple mitochondrial dysfunctions syndrome.

Shukla A, Hebbar M, Srivastava A, Kadavigere R, Upadhyai P, Kanthi A, Brandau O, Bielas S, Girisha KM.

J Hum Genet. 2017 Jul;62(7):723-727. doi: 10.1038/jhg.2017.35. Epub 2017 Mar 30.

PubMed [citation]
PMID:
28356563
PMCID:
PMC5484744

Report of the Third Family with Multiple Mitochondrial Dysfunctions Syndrome 5 Caused by the Founder Variant p.(Glu87Lys) in ISCA1.

Shukla A, Kaur P, Girisha KM.

J Pediatr Genet. 2018 Sep;7(3):130-133. doi: 10.1055/s-0038-1641177. Epub 2018 Apr 5.

PubMed [citation]
PMID:
30105122
PMCID:
PMC6087475
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000588867.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 unrelated probands of Indian descent with multiple mitochondrial dysfunctions syndrome-5 (MMDS5; 617613), Shukla et al. (2017) identified a homozygous c.259G-A transition (c.259G-A, NM_030940.3) in exon 4 of the ISCA1 gene, resulting in a glu87-to-lys (E87K) substitution at a conserved residue in the Fe-S biogenesis domain. Molecular modeling predicted that the mutation would lead to destabilization of the protein. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. The mutation was not found in homozygous state in the 1000 Genomes Project or the Exome Variant Server databases or in an in-house exome database of 139 individuals from the same population; however, the variant was found at very low frequencies in heterozygous state in the ExAC and gnomAD databases. Both probands had a similarly affected sib, although biologic material was not available from the sibs. All of the children were deceased at the time of the report. Haplotype analysis suggested a founder effect. Functional studies of the variant and studies of patient cells were not performed.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000999924.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

Apparent founder variant in southwestern India

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV001963618.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV004235809.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 16, 2024