10-66927082-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_178011.5(LRRTM3):c.166C>A(p.Pro56Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178011.5 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRTM3 | NM_178011.5 | c.166C>A | p.Pro56Thr | missense_variant | 2/3 | ENST00000361320.5 | NP_821079.3 | |
CTNNA3 | NM_013266.4 | c.1048-151558G>T | intron_variant | ENST00000433211.7 | NP_037398.2 | |||
LOC101928961 | NR_111911.1 | n.2718-16589G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRTM3 | ENST00000361320.5 | c.166C>A | p.Pro56Thr | missense_variant | 2/3 | 1 | NM_178011.5 | ENSP00000355187 | P1 | |
CTNNA3 | ENST00000433211.7 | c.1048-151558G>T | intron_variant | 1 | NM_013266.4 | ENSP00000389714 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251372Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135864
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.166C>A (p.P56T) alteration is located in exon 2 (coding exon 2) of the LRRTM3 gene. This alteration results from a C to A substitution at nucleotide position 166, causing the proline (P) at amino acid position 56 to be replaced by a threonine (T). 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