14-102376751-CAG-C
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_014844.5(TECPR2):c.35_36delAG(p.Glu12ValfsTer61) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000186 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_014844.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.35_36delAG | p.Glu12ValfsTer61 | frameshift_variant | Exon 2 of 20 | ENST00000359520.12 | NP_055659.2 | |
TECPR2 | NM_001172631.3 | c.35_36delAG | p.Glu12ValfsTer61 | frameshift_variant | Exon 2 of 17 | NP_001166102.1 | ||
LOC124903389 | XR_007064350.1 | n.73-6268_73-6267delCT | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.35_36delAG | p.Glu12ValfsTer61 | frameshift_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | ||
TECPR2 | ENST00000558678.1 | c.35_36delAG | p.Glu12ValfsTer61 | frameshift_variant | Exon 2 of 17 | 1 | ENSP00000453671.1 | |||
TECPR2 | ENST00000561228.1 | n.163_164delAG | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461874Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74360
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 49 Pathogenic:2
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This sequence change creates a premature translational stop signal (p.Glu12Valfs*61) in the TECPR2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TECPR2 are known to be pathogenic (PMID: 23176824, 25590979). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TECPR2-related conditions. For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at