14-102376788-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014844.5(TECPR2):āc.67A>Gā(p.Ile23Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,614,090 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 (ā ).
Frequency
Consequence
NM_014844.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.67A>G | p.Ile23Val | missense_variant | Exon 2 of 20 | ENST00000359520.12 | NP_055659.2 | |
TECPR2 | NM_001172631.3 | c.67A>G | p.Ile23Val | missense_variant | Exon 2 of 17 | NP_001166102.1 | ||
LOC124903389 | XR_007064350.1 | n.73-6303T>C | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.67A>G | p.Ile23Val | missense_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | ||
TECPR2 | ENST00000558678.1 | c.67A>G | p.Ile23Val | missense_variant | Exon 2 of 17 | 1 | ENSP00000453671.1 | |||
TECPR2 | ENST00000561228.1 | n.195A>G | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251468Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135914
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 727248
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74354
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 49 Uncertain:2
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This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 23 of the TECPR2 protein (p.Ile23Val). This variant is present in population databases (rs776524033, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with TECPR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 580029). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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