11-62671858-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001085372.3(UQCC3):c.113T>C(p.Met38Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001085372.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UQCC3 | NM_001085372.3 | c.113T>C | p.Met38Thr | missense_variant | Exon 1 of 2 | ENST00000377953.4 | NP_001078841.1 | |
LBHD1 | NM_024099.5 | c.-305A>G | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000354588.8 | NP_077004.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UQCC3 | ENST00000377953.4 | c.113T>C | p.Met38Thr | missense_variant | Exon 1 of 2 | 1 | NM_001085372.3 | ENSP00000367189.3 | ||
LBHD1 | ENST00000354588.8 | c.-305A>G | 5_prime_UTR_variant | Exon 1 of 7 | 1 | NM_024099.5 | ENSP00000346600.3 | |||
UQCC3 | ENST00000531323.1 | c.113T>C | p.Met38Thr | missense_variant | Exon 2 of 3 | 3 | ENSP00000432692.1 | |||
LBHD1 | ENST00000528862.2 | c.93+269A>G | intron_variant | Intron 1 of 2 | 3 | ENSP00000434489.2 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 151958Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000602 AC: 15AN: 249030Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135248
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461796Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727204
GnomAD4 genome AF: 0.000191 AC: 29AN: 152076Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 38 of the UQCC3 protein (p.Met38Thr). This variant is present in population databases (rs376452919, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with UQCC3-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at