chr18-23135916-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001100619.3(CABLES1):c.154C>T(p.Pro52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000106 in 944,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P52R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001100619.3 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 |
---|---|---|---|---|---|---|---|---|
CABLES1 | NM_001100619.3 | c.154C>T | p.Pro52Ser | missense_variant | Exon 1 of 10 | ENST00000256925.12 | NP_001094089.1 | |
CABLES1 | NM_001256438.1 | c.-137+1246C>T | intron_variant | Intron 1 of 9 | NP_001243367.1 | |||
CABLES1 | NR_023359.2 | n.88+1265C>T | intron_variant | Intron 1 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CABLES1 | ENST00000256925.12 | c.154C>T | p.Pro52Ser | missense_variant | Exon 1 of 10 | 1 | NM_001100619.3 | ENSP00000256925.7 | ||
CABLES1 | ENST00000400473.6 | c.-137+1246C>T | intron_variant | Intron 1 of 9 | 2 | ENSP00000383321.2 | ||||
CABLES1 | ENST00000580153.5 | c.-221+371C>T | intron_variant | Intron 1 of 3 | 5 | ENSP00000461994.1 | ||||
CABLES1 | ENST00000579963.5 | n.-137+1265C>T | intron_variant | Intron 1 of 6 | 2 | ENSP00000464435.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000106 AC: 1AN: 944998Hom.: 0 Cov.: 30 AF XY: 0.00000222 AC XY: 1AN XY: 449606
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154C>T (p.P52S) alteration is located in exon 1 (coding exon 1) of the CABLES1 gene. This alteration results from a C to T substitution at nucleotide position 154, causing the proline (P) at amino acid position 52 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.