7-98217762-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015395.3(TECPR1):c.3314G>A(p.Gly1105Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015395.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR1 | NM_015395.3 | c.3314G>A | p.Gly1105Glu | missense_variant | Exon 25 of 26 | ENST00000447648.7 | NP_056210.1 | |
TECPR1 | XM_005250253.5 | c.3314G>A | p.Gly1105Glu | missense_variant | Exon 25 of 26 | XP_005250310.1 | ||
TECPR1 | XM_017011937.2 | c.3212G>A | p.Gly1071Glu | missense_variant | Exon 24 of 25 | XP_016867426.1 | ||
TECPR1 | XM_047420119.1 | c.3212G>A | p.Gly1071Glu | missense_variant | Exon 24 of 25 | XP_047276075.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3314G>A (p.G1105E) alteration is located in exon 25 (coding exon 23) of the TECPR1 gene. This alteration results from a G to A substitution at nucleotide position 3314, causing the glycine (G) at amino acid position 1105 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at