NC_012920.1(MT-TL1):m.3291T>C AND Juvenile myopathy, encephalopathy, lactic acidosis AND stroke

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: May 30, 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:: RCV000850711.4

Allele description [Variation Report for NC_012920.1(MT-TL1):m.3291T>C]

NC_012920.1(MT-TL1):m.3291T>C

Genes:

MT-ND1:mitochondrially encoded NADH dehydrogenase 1 [Gene - OMIM - HGNC]
MT-TL1:mitochondrially encoded tRNA leucine 1 (UUA/G) [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Genomic location:

Preferred name:

NC_012920.1(MT-TL1):m.3291T>C

HGVS:

NC_012920.1:m.3291T>C
NC_012920.1:g.3291T>C
m.3291T>C

Links:

Genetic Testing Registry (GTR): GTR000500597; Genetic Testing Registry (GTR): GTR000556568; dbSNP: rs869312463

NCBI 1000 Genomes Browser:

rs869312463

Condition(s)

Name:: Juvenile myopathy, encephalopathy, lactic acidosis AND stroke (MELAS)
Synonyms:: Mitochondrial encephalomyopathy lactic acidosis and stroke-like episodes; MELAS syndrome
Identifiers:: MONDO: MONDO:0010789; MedGen: C0162671; Orphanet: 550; OMIM: 540000

Recent activity

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lipase maturation factor 1 [Mus musculus]
lipase maturation factor 1 [Mus musculus]
gi|254939582|ref|NP_083900.3|

Protein
RecName: Full=Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1; AltName: F...
RecName: Full=Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1; AltName: Full=Peptidyl-prolyl cis-trans isomerase Pin1; Short=PPIase Pin1
gi|20139259|sp|Q9QUR7.1|PIN1_MOUSE

Protein
serum amyloid A-4 protein precursor [Bos taurus]
serum amyloid A-4 protein precursor [Bos taurus]
gi|94966809|ref|NP_001035595.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000992944	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine	criteria provided, single submitter (Modified ACMG Guidelines (Unpublished))	Pathogenic (Jul 12, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 7520241, 31965079 Citation Link,
SCV002517712	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link,
SCV004042644	GeneReviews	no classification provided	not provided	maternal	literature only	PubMed (1) [See all records that cite this PMID]
SCV005073762	Laboratory of Prof. Karen Avraham, Tel Aviv University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 30, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	unknown	not provided	not provided	not provided	not provided	not provided	literature only
Jewish	germline	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

Interpretation of mitochondrial tRNA variants.

Wong LC, Chen T, Wang J, Tang S, Schmitt ES, Landsverk M, Li F, Wang Y, Zhang S, Zhang VW, Craigen WJ.

Genet Med. 2020 May;22(5):917-926. doi: 10.1038/s41436-019-0746-0. Epub 2020 Jan 22. Erratum in: Genet Med. 2020 May;22(5):979. doi: 10.1038/s41436-020-0770-0. Genet Med. 2020 Jun;22(6):1130. doi: 10.1038/s41436-020-0802-9.

PubMed [citation]

PMID:: 31965079

A new point mutation at nucleotide pair 3291 of the mitochondrial tRNA(Leu(UUR)) gene in a patient with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS).

Goto Y, Tsugane K, Tanabe Y, Nonaka I, Horai S.

Biochem Biophys Res Commun. 1994 Aug 15;202(3):1624-30.

PubMed [citation]

PMID:: 7520241

See all PubMed Citations (3)

Details of each submission

From Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine, SCV000992944.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The NC_012920.1:m.3291T>C variant in MT-TL1 gene is interpreted to be a Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: PS3, PS5

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV002517712.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneReviews, SCV004042644.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Prof. Karen Avraham, Tel Aviv University, SCV005073762.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Jewish	1	not provided	not provided	research	PubMed (1)

Description

Pathogenic according to ClinVar based on PMID: 23273904, 20301411

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Aug 25, 2024

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