Variant: NC_012920.1(MT-TI):m.4295A>G

CA254841

9603 (ClinVar)

Gene: N/A

Condition: mitochondrial disease

Inheritance Mode: Mitochondrial inheritance

UUID: abcf56d8-bb12-4b29-86c0-458b4b0e2e85

Approved on: 2023-12-11

Published on: 2025-03-12

HGVS expressions

NC_012920.1:m.4295A>G
J01415.2:m.4295A>G

Uncertain Significance

• Met criteria codes: PS4_Moderate PS3_Moderate

• Not Met criteria codes: BS1 BP4 PP1 PP3 BA1 PM2

Expert Panel

Mitochondrial Diseases VCEP

Criteria Specification Information

Criteria Specification: ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_mtDNA

Evidence submitted by expert panel

Mitochondrial Diseases VCEP

The m.4295A>G variant in MT-TI has been reported in at least four families from different ethnic groups with features of primary mitochondrial disease including deafness, hearing loss, and cardiomyopathy (PMIDs: 18177739, 22241583, 33398350, 34991096, 8889580; PS4_moderate). Of note, other isolated phenotypes have been reported including essential hypertension and autism spectrum disorder, but these are outside the scope of this curation (PMIDs: 11406419, 19778529, 19043581). This variant is seen in the general population (<0.5% in three large population databases: Mitomap - 112/61168, gnomAD v3.1.2 - 167/56431, and Helix - 923/195983). Notably, these occurrences are almost exclusively in haplogroup (hg) K (110/112 in specifically K1a in Mitomap; 166/167 in hg K in gnomAD, 911/923 in K in Helix) and these three databases combined reported only 15 individuals from non-K haplogroups (H, I, R, X, J, U, and V). In silico predictors are conflicting as the computational predictor MitoTIP suggests this variant is possibly benign (0.44) but HmtVAR predicts it to be pathogenic (0.75). Of note, this variant is 100% conserved among 45 species ranging from Drosophila to Homo sapiens in the extraordinarily conserved anticodon loop of tRNA Isoleucine. Cybrid studies showed multiple deleterious biochemical impacts of the variant in a Chinese family from haplogroup D4j (PMID: 33398350). Other studies showed this variant reduces the efficiency with which tRNAIle can be processed by 3′-tRNase (PMID: 18177739). An in-vitro system utilizing plasmids with tRNAIle inserts showed that this variant reduces the tRNase Z reaction 10.3-fold (PMID: 12655007). On the basis of these strong, independent, and consistent functional studies, this Expert Panel elected to give higher weight to this line of evidence (PS3_moderate). In summary, this variant meets criteria to be classified as uncertain significance for primary mitochondrial disease inherited in a mitochondrial manner. We note there was much discussion of the possible differing roles of this variant in haplogroups K1a (protective or tolerated) and D4j (damaging), however the VCEP elected to keep the classification of this variant as uncertain significance (four of 11 experts felt likely benign was the more appropriate classification). This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Variant Curation Expert Panel on December 11, 2023. Mitochondrial DNA-specific ACMG/AMP criteria applied (PMID: 32906214): PS4_moderate, PS3_moderate.

Met criteria codes

• PS4_Moderate: The m.4295A>G variant in MT-TI has been reported in at least four families from different ethnic groups who had features of primary mitochondrial disease including deafness, hearing loss, and cardiomyopathy (PMIDs: 18177739, 22241583, 33398350, 34991096, 8889580; PS4_moderate).
• PS3_Moderate: Cybrid studies showed multiple deleterious biochemical impacts of the variant in a Chinese family from haplogroup D4j (PMID: 33398350). Other studies showed this variant reduces the efficiency with which tRNAIle can be processed by 3′-tRNase (PMID: 18177739). An in-vitro system utilizing plasmids with tRNAIle inserts showed that this variant reduces the tRNase Z reaction 10.3-fold (PMID: 12655007). On the basis of these strong, independent, and consistent functional studies, this Expert Panel elected to give higher weight to this line of evidence (PS3_moderate).

Not Met criteria codes

• BS1: m.4925A>G does not meet BA1 or BS1 but it should be noted that it is found almost exclusively in top level hg K, specifically subgroup K1a. Although not a marker, at the top level K it is seen at>6% in gnomAD and Helix and at >5% in Mitomap. In subgroup K1a it is found at 8.45%, in Mitomap and 12.33% in Helix.
• BP4: The in-silico predictor MitoTip scores m.4295A>G as “Possibly Benign” with a score of 0.44. PON-mt-tRNA scores this variant as 0.4 - likely neutral However, HmtVar scores variant m.4295A>G at 0.75, “Pathogenic”. Using the scoring system of Yarham et al 2011 [PMID 21882289] this variant comes to “Pathogenic” at 15/20 when adding the later cybrid study of Gutierrez Cortes et al 2012 [PMID 22241583].
• PP1: The 1998 Merante study (PMID 8889580) reported heteroplasmy but with varying levels in different tissues. Unfortunately, the tested tissues were not the same between the proband and other family members, and the PCR/RFLP quantification used old technology which had a high probability for inaccuracy.
• PP3: HmtVar scores variant m.4295A>G at 0.75, “Pathogenic”. Using the scoring system of Yarham et al 2011 [PMID 21882289] this variant comes to “Pathogenic” at 15/20 when adding the later cybrid study of Gutierrez Cortes et al 2012 [PMID 22241583]. However, The in-silico predictor MitoTip scores m.4295A>G as “Possibly Benign” with a score of 0.44. PON-mt-tRNA scores this variant as 0.4 - likely neutral
• BA1: m.4925A>G does not meet BA1 or BS1 but it should be noted that it is found almost exclusively in top level hg K, specifically subgroup K1a. Although not a marker, at the top level K it is seen at>6% in gnomAD and Helix and at >5% in Mitomap. In subgroup K1a it is found at 8.45%, in Mitomap and 12.33% in Helix.
• PM2: m.4295A>G is found at an overall frequency of 0.183%, 0.296%, 0.0.471% in Mitomap, gnomAD, and Helix respectively.