chr11-74003846-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003356.4(UCP3):c.805C>T(p.Pro269Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003356.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UCP3 | NM_003356.4 | c.805C>T | p.Pro269Ser | missense_variant | 6/7 | ENST00000314032.9 | |
UCP3 | NM_022803.3 | c.805C>T | p.Pro269Ser | missense_variant | 6/6 | ||
UCP3 | XM_047427519.1 | c.805C>T | p.Pro269Ser | missense_variant | 5/6 | ||
UCP3 | XR_007062495.1 | n.1008C>T | non_coding_transcript_exon_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UCP3 | ENST00000314032.9 | c.805C>T | p.Pro269Ser | missense_variant | 6/7 | 1 | NM_003356.4 | P1 | |
UCP3 | ENST00000426995.2 | c.805C>T | p.Pro269Ser | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248180Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134052
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457024Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 724374
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 24, 2022 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with UCP3-related conditions. This variant is present in population databases (rs781146737, gnomAD 0.003%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 269 of the UCP3 protein (p.Pro269Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at