chr6-1610483-T-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001453.3(FOXC1):āc.38T>Cā(p.Leu13Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000134 in 1,493,636 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.
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 31)
Exomes š: 7.4e-7 ( 0 hom. )
Consequence
FOXC1
NM_001453.3 missense
NM_001453.3 missense
Scores
9
7
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.13
Genes affected
FOXC1 (HGNC:3800): (forkhead box C1) This gene belongs to the forkhead family of transcription factors which is characterized by a distinct DNA-binding forkhead domain. The specific function of this gene has not yet been determined; however, it has been shown to play a role in the regulation of embryonic and ocular development. Mutations in this gene cause various glaucoma phenotypes including primary congenital glaucoma, autosomal dominant iridogoniodysgenesis anomaly, and Axenfeld-Rieger anomaly. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.794
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXC1 | NM_001453.3 | c.38T>C | p.Leu13Pro | missense_variant | Exon 1 of 1 | ENST00000645831.2 | NP_001444.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 151086Hom.: 0 Cov.: 31
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GnomAD4 exome AF: 7.45e-7 AC: 1AN: 1342550Hom.: 0 Cov.: 31 AF XY: 0.00000152 AC XY: 1AN XY: 658702
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GnomAD4 genome AF: 0.00000662 AC: 1AN: 151086Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73770
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
.;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;.
REVEL
Pathogenic
Sift
Pathogenic
D;.
Sift4G
Benign
T;.
Polyphen
D;D
Vest4
MutPred
Gain of disorder (P = 0.0043);Gain of disorder (P = 0.0043);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at