rs199474661

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate

Variant has been reported in ClinVar as Likely pathogenic (★).

Frequency

Mitomap GenBank:
Absent

Consequence

TRNL1
missense

Scores

Mitotip
Uncertain
11

Clinical Significance

Likely pathogenic criteria provided, single submitter P:2O:1
MELAS,EXIT

Conservation

PhyloP100: 6.99
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
No frequency data in Mitomap. Probably very rare.
PP5
Variant M-3252-A-G is Pathogenic according to our data. Variant chrM-3252-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 9594.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRNL1unassigned_transcript_4789 use as main transcriptc.23A>G p.Asn8Ser missense_variant 1/1
RNR2unassigned_transcript_4788 use as main transcriptn.*23A>G downstream_gene_variant
use as main transcript

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap

MELAS,EXIT

ClinVar

Significance: Likely pathogenic
Submissions summary: Pathogenic:2Other:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

MELAS syndrome Pathogenic:1Other:1
not provided, no classification providedliterature onlyGeneReviews-- -
Likely pathogenic, criteria provided, single submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineJul 12, 2019The NC_012920.1:m.3252A>G variant in MT-TL1 gene is interpreted to be a Likely Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: PM8, PM9, PM10 -
Mitochondrial encephalomyopathy Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMDec 01, 1993- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
11
Hmtvar
Pathogenic
0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs199474661; hg19: chrM-3253; API