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NC_012920.1(MT-ND4):m.11778G>A AND Leber optic atrophy

Germline classification:
Pathogenic (13 submissions)
Last evaluated:
Feb 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000010354.24

Allele description [Variation Report for NC_012920.1(MT-ND4):m.11778G>A]

NC_012920.1(MT-ND4):m.11778G>A

Gene:
MT-ND4:mitochondrially encoded NADH dehydrogenase 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Genomic location:
Preferred name:
NC_012920.1(MT-ND4):m.11778G>A
HGVS:
  • NC_012920.1:m.11778G>A
  • AC_000021.2:m.11778G>A
  • NC_012920.1:g.11778G>A
  • m.11778G>A
Links:
Genetic Testing Registry (GTR): GTR000500596; Genetic Testing Registry (GTR): GTR000501208; Genetic Testing Registry (GTR): GTR000522506; OMIM: 516003.0001; dbSNP: rs199476112
NCBI 1000 Genomes Browser:
rs199476112
Observations:
1

Condition(s)

Name:
Leber optic atrophy (LHON)
Synonyms:
Optic Atrophy, Hereditary, Leber; Leber hereditary optic neuropathy; Leber's disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010788; MedGen: C0917796; Orphanet: 104; OMIM: 535000; Human Phenotype Ontology: HP:0001112

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000030580OMIM
no assertion criteria provided
Pathogenic
(Dec 1, 2008)
germlineliterature only

PubMed (41)
[See all records that cite these PMIDs]

SCV000086616GeneReviews
no classification provided
not providedmaternalliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000784691GenomeConnect, ClinGen
no classification provided
not providedunknownphenotyping only

SCV000894486Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 31, 2018)
unknownclinical testing

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

SCV000993412Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
no assertion criteria provided
Pathogenic
(Jun 26, 2018)
maternalresearch

SCV000997789Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
criteria provided, single submitter

(Modified ACMG Guidelines (Unpublished))
Pathogenic
(Oct 17, 2019)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV001745880Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicmaternalclinical testing

SCV001760532Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)
Pathogenicgermlineclinical testing

Citation Link,

SCV002011706Clinical Genetics Laboratory, University Hospital Schleswig-Holstein
no assertion criteria provided
Pathogenic
(Sep 16, 2021)
germlineclinical testing

SCV002517671Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Pathogenic
(May 4, 2022)
germlineclinical testing

Citation Link,

SCV002526724Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 1, 2024)
unknownclinical testing

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

SCV002761214Pediatric Department, Xiangya Hospital, Central South University
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicmaternalclinical testing

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

SCV003922001Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicmaternalclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedmaternalyes1not providednot providednot providednot providedclinical testing, research
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing, phenotyping only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedmaternalunknownnot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy.

Wallace DC, Singh G, Lott MT, Hodge JA, Schurr TG, Lezza AM, Elsas LJ 2nd, Nikoskelainen EK.

Science. 1988 Dec 9;242(4884):1427-30.

PubMed [citation]
PMID:
3201231

A mitochondrial DNA mutation as a cause of Leber's hereditary optic neuropathy.

Singh G, Lott MT, Wallace DC.

N Engl J Med. 1989 May 18;320(20):1300-5.

PubMed [citation]
PMID:
2566116
See all PubMed Citations (44)
PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]
PMCID:
PMC4544753
PMID:
25741868
DOI:
10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000030580.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (41)

Description

The allele changes the highly conserved arginine at amino acid 340 to a histidine (R340H). This allele accounts for over 50% of Leber hereditary optic neuropathy (LHON; 535000) cases among Caucasians and over 90% of the cases in Asians. The mutation has not been observed in random population controls, may be either homoplasmic or heteroplasmic within families, and has been shown to have arisen multiple times on different mtDNA haplotypes in association with the disease (Wallace et al., 1988; Singh et al., 1989). In families harboring this mutation, approximately 33 to 60% of the maternal relatives are affected and of these, about 80% are males. Visual recovery is seen in only 4% of cases (see LHON Table, MIM11 foreword section) (Bolhuis et al., 1990; Carducci et al., 1991; Cavelier et al., 1993; Cortelli et al., 1991; Cullom et al., 1993; Erickson and Castora, 1993; Hiida et al., 1991, 1992; Holt et al., 1989; Hotta et al., 1989; Howell et al., 1992; Huoponen et al., 1990; Isashiki and Nakagawa, 1991; Johns, 1990; Johns and Berman, 1991; Johns et al., 1992, 1993; Kormann et al., 1991; Larsson et al., 1991; Lott et al., 1990; Majander et al., 1991; Mashima et al., 1992, 1993; Moorman et al., 1993; Nakamura et al., 1993; Newman, 1993; Newman et al., 1991; Newman and Wallace, 1990; Norby, 1993; Poulton et al., 1991; Singh et al., 1989; Smith et al., 1993; Stone et al., 1990, 1992; Sudoyo et al., 1992; Vilkki et al., 1989, 1990; Wallace et al., 1988; Weiner et al., 1993; Yoneda et al., 1989; Zhu et al., 1992).

In 37 Italian subjects with LHON, Torroni et al. (1997) found that 28 were 11778-positive, 7 were 3460-positive (516000.0001) and 2 were 14484-positive (516006.0001). High-resolution restriction endonuclease analysis was also performed in all subjects in order to define the phylogenetic relationships between mtDNA haplotypes and LHON mutations. Ninety-nine Italian controls were screened for mutations and haplotypes. The analysis showed that the putative secondary/intermediate LHON mutations 4216, 4917, 13708, 15257, and 15812 are ancient polymorphisms, are associated in specific combinations, and define 2 common Caucasoid-specific haplotype groupings, designated haplogroups J and T. On the contrary, the same analysis showed that the primary mutations 11778, 3460, and 14484 are recent and are due to multiple mutational events. However, phylogenetic analysis revealed a different evolutionary pattern for the 3 primary mutations. The 3460 mutations were distributed randomly along with phylogenetic trees, without any preferential association with the 9 haplotypes that characterize European populations, whereas the 11778 and 14484 mutations showed a strong preferential association with haplotype J. The findings suggested that one ancient combination of haplotype J with specific mutations increases the penetrance of the 2 primary mutations 11778 and 14484.

Chinnery et al. (2001) analyzed 17 independent pedigrees that harbored the 11778G-A mutation. They made the following observations: (1) The frequency of blindness in males was related to the mutation load in the individual's blood. (2) Mothers with 80% or less mutant mtDNA in blood were less likely to have clinically affected sons than mothers with 100% mutant mtDNA in their blood. (3) Within individual lineages, changes in mutation load from one generation to the next were largely determined by random genetic drift.

Wong et al. (2002) created cybrids using a neuronal precursor cell line, NT2, containing mitochondria from patient lymphoblasts bearing the most common LHON mutation, 11778, and the most severe LHON mutation, 3460 (516000.0001). The undifferentiated LHON-NT2 mutant cells were not significantly different from the parental cell control in terms of mtDNA/nDNA ratio, mitochondrial membrane potential, reactive oxygen species (ROS) production, or the ability to reduce the reagent Alamar blue. Differentiation of NT2s resulted in a neuronal morphology, a neuron-specific pattern of gene expression, and a 3-fold reduction in mtDNA/nDNA ratio in both mutant and control cells; however, the differentiation protocol yielded 30% less LHON cells than controls, indicating either a decreased proliferative potential or increased cell death of the LHON-NT2 cells. Differentiation of the cells to the neuronal form also resulted in significant increases in ROS production in the LHON-NT2 neurons versus controls, which was abolished by rotenone (a specific inhibitor of complex I). Wong et al. (2002) inferred that the LHON genotype may require a differentiated neuronal environment in order to induce increased mitochondrial ROS, which may be the cause of the reduced NT2 yield. They hypothesized that the LHON degenerative phenotype may be the result of an increase in mitochondrial superoxide which is caused by the LHON mutations, possibly mediated through neuron-specific alterations in complex I structure.

Guy et al. (2002) found that cybrid cells containing the 11778G-A mutation showed a 60% reduction in the rate of complex I-dependent ATP synthesis compared to wildtype cells. Using 'allotopic expression,' a technique in which a mitochondrial gene is expressed in the nucleus and the protein product is then imported back to the mitochondria, Guy et al. (2002) transfected a fusion ND4 subunit gene into cybrids containing the 11778G-A mutation. Cybrid cell survival after 3 days was 3-fold greater for the allotopically transfected cells, and these cells showed a 3-fold increase in the rate of complex I-dependent ATP synthesis, to a level indistinguishable from that in normal cybrids. Guy et al. (2002) suggested that this rescue of a severe oxidative phosphorylation deficiency held promise for development of gene therapy for mitochondrial disorders.

Mimaki et al. (2003) reported a male patient with LHON and cardiomyopathy who had the 11778G-A mutation as well as a 12192G-A mutation in the MTTH gene (590040.0001), which is a risk factor for cardiomyopathy. Because no case of LHON presenting with cardiomyopathy had previously been reported, the findings suggested that this was an instance of double pathogenic mtDNA mutations associated either synergistically or concomitantly with 2 different clinical manifestations.

In a study of 87 index cases with LHON sequentially diagnosed in Italy, including an extremely large Brazilian family of Italian maternal ancestry, 67 subjects had the 11778/ND4 mutation. Carelli et al. (2006) concluded that the large majority of LHON mutations were due to independent mutational events. In the 87 index cases, only 7 pairs and 3 triplets of identical haplotypes were observed. Assignment of the mutational events into haplogroups confirmed that J1 and J2 play a role in LHON expression but narrowed the association to the subclades J1c and J2b, thus suggesting that 2 specific combinations of amino acid changes in cytochrome b (516020) are the cause of the mtDNA background effect and that this may occur at the level of the supercomplex formed by respiratory chain complexes I and III.

Phasukkijwatana et al. (2006) examined 30 unrelated pedigrees of Thai or Chinese origin with LHON and the 11778G-A mutation. Compared to Caucasian and Japanese populations with the same mutation, the pedigrees in the study showed a lower male-to-female ratio (2.6:1) of affected persons and a higher prevalence of blood heteroplasmy (37% of the pedigrees contained at least 1 heteroplasmic 11778G-A individual). The estimated overall penetrance was 37% for males and 13% for females.

In affected members of a 3-generation Chinese family that exhibited high penetrance and expressivity of visual impairment due to LHON, Qu et al. (2006) identified the homoplasmic 11778G-A mutation and 35 other variants in the MTND4 gene belonging to the Asian haplogroup D5. One of the other variants, a novel homoplasmic 4435A-G mutation, which is localized at the 3-prime end adjacent to the anticodon, at conventional position 37 (A37), was absent in 164 Chinese controls. A37 in MTND4 is extraordinarily conserved from bacteria to human mitochondria. The modified A37 was shown to contribute to the high fidelity of codon recognition and to the structural formation and stabilization of functional tRNAs. A significant reduction of the steady state levels in tRNA-Met was observed in cells carrying both the 4435A-G and 11778G-A mutations but not in cells carrying only the 11778G-A mutation. Thus, a failure in mitochondrial tRNA metabolism, caused by the 4435A-G mutation, might worsen the mitochondrial dysfunction associated with the primary 11778G-A mutation. Qu et al. (2006) concluded that the novel 4435A-G mutation had a potential modifier role in increasing the penetrance and expressivity of the primary LHON-associated G11778A mutation in the Chinese family.

To create an animal model of LHON, Ellouze et al. (2008) introduced the human ND4 gene harboring the 11778G-A mutation, responsible for 60% of LHON cases, into rat eyes by in vivo electroporation. The treatment induced the degeneration of retinal ganglion cells, which were 40% less abundant in treated eyes than in control eyes. This deleterious effect was also confirmed in primary cell culture, in which both RGC survival and neurite outgrowth were compromised. Importantly, RGC loss was clearly associated with a decline in visual performance. A subsequent electroporation with wildtype ND4 prevented both RGC loss and the impairment of visual function. Ellouze et al. (2008) concluded that their data provided the proof of principle that optimized allotopic expression can be an effective treatment for LHON, and that they opened the way to clinical studies of other devastating mitochondrial disorders.

By studying the penetrance of LHON in 1,859 individuals from 182 Chinese families (including 1 from Cambodia) with the MTND4 11778G-A mutation, Ji et al. (2008) found that mitochondrial haplogroup M7b1-prime-2 was associated with increased risk of visual loss, whereas the M8a haplogroup was associated with decreased risk of visual loss. Further sequence analysis suggested that the M7b1-prime-2 effect was due to variation in the MTND5 (516005) gene, and that the M8a effect was due to variation in the MTATP6 gene (516060).

See LOAM (308905) for discussion of a form of LHON with increased penetrance and earlier age of onset resulting from additional mutation in the PRICKLE3 gene (300111.0001) acting as a modifier of disease expression.

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

From GeneReviews, SCV000086616.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

This variant is one of the three most common causes of LHON.

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

From GenomeConnect, ClinGen, SCV000784691.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedphenotyping onlynot provided

Description

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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

From Fulgent Genetics, Fulgent Genetics, SCV000894486.1

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

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV000993412.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot provided1not providednot providednot provided

From Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine, SCV000997789.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The NC_012920.1:m.11778G>A (YP_003024035.1:p.Arg340His) variant in MTND4 gene is interpretated to be a Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: PS1, PS4

#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, SCV001745880.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

From Genomics England Pilot Project, Genomics England, SCV001760532.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics Laboratory, University Hospital Schleswig-Holstein, SCV002011706.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV002517671.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002526724.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria applied: PS4,PM5,PP1_MOD,PS3_SUP,PP3

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

From Pediatric Department, Xiangya Hospital, Central South University, SCV002761214.1

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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV003922001.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

A heteroplasmic (76.20%) missense variant has been identified in MT-ND4. This gene encodes a protein subunit of complex I. The variant is predicted to result in a minor amino acid change from arginine to histidine at position 340 of the protein. The arginine at this position has high conservation (MITOMASTER). In silico predictions for this variant are consistently pathogenic (Polyphen, SIFT, HmtDB Disease Score). The variant is present in the MITOMAP population database at a frequency of 0.358%. The variant has been previously described as pathogenic in multiple individuals with Leber hereditary optic neuropathy (LHON) and is considered to be the most common MT-ND4 variant in European and Asian populations. Affected individuals generally have more than 70% heteroplasmy in blood, however the variant is also known to have reduced penetrance, with males more commonly affected than females (ClinVar, GeneReviews, OMIM, PMID: 31932089). This variant has been shown to be maternally inherited (by trio analysis) with a heteroplamic level of 26.70% in this individual's mother.

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

Last Updated: Sep 16, 2024