1-203772137-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017773.4(LAX1):c.380C>T(p.Pro127Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,612,588 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017773.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAX1 | NM_017773.4 | c.380C>T | p.Pro127Leu | missense_variant | Exon 4 of 5 | ENST00000442561.7 | NP_060243.2 | |
LAX1 | NM_001136190.2 | c.332C>T | p.Pro111Leu | missense_variant | Exon 4 of 5 | NP_001129662.1 | ||
LAX1 | NM_001282878.1 | c.152C>T | p.Pro51Leu | missense_variant | Exon 4 of 5 | NP_001269807.1 | ||
LAX1 | XM_006711397.4 | c.380C>T | p.Pro127Leu | missense_variant | Exon 5 of 6 | XP_006711460.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAX1 | ENST00000442561.7 | c.380C>T | p.Pro127Leu | missense_variant | Exon 4 of 5 | 1 | NM_017773.4 | ENSP00000406970.2 | ||
LAX1 | ENST00000367215.1 | n.350C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 1 | |||||
LAX1 | ENST00000367217.5 | c.332C>T | p.Pro111Leu | missense_variant | Exon 4 of 5 | 2 | ENSP00000356186.5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251286Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135796
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460486Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 726602
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.380C>T (p.P127L) alteration is located in exon 4 (coding exon 4) of the LAX1 gene. This alteration results from a C to T substitution at nucleotide position 380, causing the proline (P) at amino acid position 127 to be replaced by a leucine (L). 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