rs1553752849
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP3
The NM_023067.4(FOXL2):c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC(p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro) variant causes a protein altering change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
FOXL2
NM_023067.4 protein_altering
NM_023067.4 protein_altering
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.32
Genes affected
FOXL2 (HGNC:1092): (forkhead box L2) This gene encodes a forkhead transcription factor. The protein contains a fork-head DNA-binding domain and may play a role in ovarian development and function. Expansion of a polyalanine repeat region and other mutations in this gene are a cause of blepharophimosis syndrome and premature ovarian failure 3. [provided by RefSeq, Jul 2016]
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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;
PP5
?
Variant 3-138946022-G-GGCGGCTGCAGCCGCAGCTGCTGCAGCCGCT is Pathogenic according to our data. Variant chr3-138946022-G-GGCGGCTGCAGCCGCAGCTGCTGCAGCCGCT is described in ClinVar as [Pathogenic]. Clinvar id is 559900.Status of the report is criteria_provided_single_submitter, 1 stars.
BP3
?
Nonframeshift variant in repetitive region in NM_023067.4
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXL2 | NM_023067.4 | c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC | p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro | protein_altering_variant | 1/1 | ENST00000648323.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXL2 | ENST00000648323.1 | c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC | p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro | protein_altering_variant | 1/1 | NM_023067.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Blepharophimosis, ptosis, and epicanthus inversus syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | Jul 29, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at