rs104893951
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM5PP3_Strong
The NM_001453.3(FOXC1):c.335T>A(p.Phe112Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F112S) has been classified as Pathogenic.
Frequency
Consequence
NM_001453.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXC1 | NM_001453.3 | c.335T>A | p.Phe112Tyr | missense_variant | 1/1 | ENST00000645831.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXC1 | ENST00000645831.2 | c.335T>A | p.Phe112Tyr | missense_variant | 1/1 | NM_001453.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151790Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251378Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135888
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727238
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151790Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74128
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at