rs281875325
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1PM2PP2PP3_StrongPP5_Very_Strong
The NM_001614.5(ACTG1):c.359C>T(p.Thr120Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T120S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001614.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTG1 | NM_001614.5 | c.359C>T | p.Thr120Ile | missense_variant | 3/6 | ENST00000573283.7 | |
ACTG1 | NM_001199954.3 | c.359C>T | p.Thr120Ile | missense_variant | 3/6 | ||
ACTG1 | NR_037688.3 | n.431C>T | non_coding_transcript_exon_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTG1 | ENST00000573283.7 | c.359C>T | p.Thr120Ile | missense_variant | 3/6 | 5 | NM_001614.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 37
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Baraitser-winter syndrome 2 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 26, 2012 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Centogene AG - the Rare Disease Company | Feb 28, 2020 | - - |
See cases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein | Nov 23, 2021 | ACMG classification criteria: PS4, PM2, PM6, PP2, PP3 - |
not provided Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at