rs796052141
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP6
The NM_014263.4(YME1L1):c.859G>A(p.Val287Met) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
YME1L1
NM_014263.4 missense, splice_region
NM_014263.4 missense, splice_region
Scores
3
7
4
Splicing: ADA: 0.9992
2
Clinical Significance
Conservation
PhyloP100: 6.77
Genes affected
YME1L1 (HGNC:12843): (YME1 like 1 ATPase) The protein encoded by this gene is the human ortholog of yeast mitochondrial AAA metalloprotease, Yme1p. It is localized in the mitochondria and can functionally complement a yme1 disruptant yeast strain. It is proposed that this gene plays a role in mitochondrial protein metabolism and could be involved in mitochondrial pathologies. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, YME1L1
BP6
?
Variant 10-27126786-C-T is Benign according to our data. Variant chr10-27126786-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 207832.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YME1L1 | NM_014263.4 | c.859G>A | p.Val287Met | missense_variant, splice_region_variant | 9/19 | ENST00000376016.8 | |
YME1L1 | NM_139312.3 | c.1030G>A | p.Val344Met | missense_variant, splice_region_variant | 10/20 | ||
YME1L1 | NM_001253866.2 | c.760G>A | p.Val254Met | missense_variant, splice_region_variant | 8/18 | ||
YME1L1 | XM_011519300.4 | c.931G>A | p.Val311Met | missense_variant, splice_region_variant | 9/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YME1L1 | ENST00000376016.8 | c.859G>A | p.Val287Met | missense_variant, splice_region_variant | 9/19 | 1 | NM_014263.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 25
GnomAD4 exome
Cov.:
25
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Long QT syndrome Benign:1
Likely benign, no assertion criteria provided | research | Medical Research Institute, Tokyo Medical and Dental University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T;T;.
Polyphen
0.38, 1.0
.;B;D;.;.
Vest4
MutPred
0.36
.;Loss of catalytic residue at V344 (P = 0.0342);.;Loss of catalytic residue at V344 (P = 0.0342);.;
MVP
MPC
1.1
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at