6-107040076-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The ENST00000311381.8(MTRES1):c.316T>C(p.Ser106Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
MTRES1
ENST00000311381.8 missense
ENST00000311381.8 missense
Scores
3
15
Clinical Significance
Conservation
PhyloP100: 2.39
Genes affected
MTRES1 (HGNC:17971): (mitochondrial transcription rescue factor 1) Enables ribosomal large subunit binding activity and tRNA binding activity. Involved in regulation of mitochondrial transcription and rescue of stalled ribosome. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM1
In a modified_residue Phosphoserine (size 0) in uniprot entity MRES1_HUMAN
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12786776).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTRES1 | NM_016487.5 | c.316T>C | p.Ser106Pro | missense_variant | 2/4 | ENST00000311381.8 | NP_057571.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTRES1 | ENST00000311381.8 | c.316T>C | p.Ser106Pro | missense_variant | 2/4 | 1 | NM_016487.5 | ENSP00000310951 | P1 | |
MTRES1 | ENST00000625458.1 | c.331T>C | p.Ser111Pro | missense_variant | 3/5 | 3 | ENSP00000485698 | |||
MTRES1 | ENST00000405204.6 | c.316T>C | p.Ser106Pro | missense_variant | 2/4 | 2 | ENSP00000384867 | P1 | ||
MTRES1 | ENST00000489790.1 | n.85T>C | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.331T>C (p.S111P) alteration is located in exon 3 (coding exon 2) of the C6orf203 gene. This alteration results from a T to C substitution at nucleotide position 331, causing the serine (S) at amino acid position 111 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
D;D;N
PROVEAN
Uncertain
N;N;.
REVEL
Benign
Sift
Benign
T;T;.
Sift4G
Benign
T;T;T
Polyphen
D;D;.
Vest4
MutPred
Loss of phosphorylation at S106 (P = 7e-04);Loss of phosphorylation at S106 (P = 7e-04);.;
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.