4-786595-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006651.4(CPLX1):c.311G>A(p.Gly104Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000403 in 1,611,998 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 (★★).
Frequency
Consequence
NM_006651.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPLX1 | ENST00000304062.11 | c.311G>A | p.Gly104Asp | missense_variant | Exon 4 of 4 | 1 | NM_006651.4 | ENSP00000305613.6 | ||
CPLX1 | ENST00000505203.1 | c.248G>A | p.Gly83Asp | missense_variant | Exon 5 of 5 | 2 | ENSP00000425960.1 | |||
CPLX1 | ENST00000504062.1 | c.266G>A | p.Gly89Asp | missense_variant | Exon 3 of 3 | 3 | ENSP00000421947.1 | |||
CPLX1 | ENST00000506404.1 | n.364G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000449 AC: 11AN: 245244Hom.: 0 AF XY: 0.0000524 AC XY: 7AN XY: 133556
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1459786Hom.: 0 Cov.: 36 AF XY: 0.0000151 AC XY: 11AN XY: 726128
GnomAD4 genome AF: 0.000289 AC: 44AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74420
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.311G>A (p.G104D) alteration is located in exon 4 (coding exon 3) of the CPLX1 gene. This alteration results from a G to A substitution at nucleotide position 311, causing the glycine (G) at amino acid position 104 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 104 of the CPLX1 protein (p.Gly104Asp). This variant is present in population databases (rs562631127, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CPLX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1411489). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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