X-136207169-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_001159702.3(FHL1):c.310T>C(p.Cys104Arg) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C104W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001159702.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FHL1 | NM_001159702.3 | c.310T>C | p.Cys104Arg | missense_variant | 4/8 | ENST00000394155.8 | |
FHL1 | NM_001159699.2 | c.358T>C | p.Cys120Arg | missense_variant | 3/6 | ENST00000370683.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FHL1 | ENST00000394155.8 | c.310T>C | p.Cys104Arg | missense_variant | 4/8 | 5 | NM_001159702.3 | ||
FHL1 | ENST00000370683.6 | c.358T>C | p.Cys120Arg | missense_variant | 3/6 | 1 | NM_001159699.2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Myopathy, reducing body, X-linked, childhood-onset Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 27, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at