chr3-138945277-TGGGCAGGAGACGCTGGGGCTCCGGAAAGAGACGAGCCCAGTAGAAAGCGCGCAGAGAGGCAGCTTCAGGCCAGGGGAGTGCAAGGTCACAGAGGTCAGGGAGGTGAGCACAGGAGGACATAAACTGAGGGGACAAAGAGGAGCGACAGGAGCTTAGGAAAGCGAAAAAGCACAGAGGGACCCTGGGCGCTGGCTCCAGAGGCGGGCCCAGAGGGTGTGAGGTCAGGCTGGCGGCGGCGTCGTCGGCTGCGACCGGGGCCGGCGTCGCGCGTCCCTGCATCCTCGCATCCGTCTGCACCGGCATGCGGTGGGCTCTCAGAGATCGAGGCGCGAATGCAGCGCGCCGGTCTTGCTGTCGTGGTCCCAGTAAGAGCAATGCATCATGGCGAGCTCGGGCTGCCGGGCACAAGCGAACTGCAGGCCCGGCGCACTGGTGGGCGCGGGCGCCGGGGGCGCGGCGGTGGCTGGGCTGGCAGGGCTGAGCTGGCCCGGCGGCGGCGCGGCGGCCCCGTGGTGCGGTGGGGCAGGCGGCGGTGCGGCGGCCGCGTGCAGATGGTGTGCGTGCGGATGCGGGTGGGGGTGCGGCGGAGGCGGGGGTGCGGCCGGCGGGCCTCCCAGGCCATTGTACGAGTTCACTACGCCGGGGGGCAGCGCCATGCTCTGCACGCGTGTGTACGGCCCGTACGAGGCGGCCGGGCCCGCCAGCCCCTTGACCACAGCGGCCGCGCCAGGGCTACCGGGGCCCGCGGCTGCAGCCGCAGCTGCTGCAGCCGC-GCGGCTGCAGCAGCTGCGGCTGCAGCCGCGGGCCCCGGTAGCCCTGGCGCGGCCGCTGTGGTCAAGGGGCTGGCGGGCCCGGCCGCCTCGTACGGGCCGTACACACGCGTGCAGAGCATGGCGCTGCCCCCCGGCGTAGTGAACTCGTACAATGGCCTGGGAGGCCCGCCGGCCGCACCCCCGCCTCCGCCGCACCCCCACCCGCATCCGCACGCACACCATCTGCACGCGGCCGCCGCACCGCCGCCTGCCCCACCGCACCACGGGGCCGCCGCGCCGCCGCCGGGCCAGCTCAGCCCTGCCAGCCCAGCCACCGCCGCGCCCCCGGCGCCCGCGCCCACCAGTGCGCCGGGCCTGCAGTTCGCTTGTGCCCGGCAGCCCGAGCTCGCCATGATGCATTGCTCTTACTGGGACCACGACAGCAAGACCGGCGCGCTGCATTCGCGCCTCGATCTCTGAGAGCCCACCGCATGCCGGTGCAGACGGATGCGAGGATGCAGGGACGCGCGACGCCGGCCCCGGTCGCAGCCGACGACGCCGCCGCCAGCCTGACCTCACACCCTCTGGGCCCGCCTCTGGAGCCAGCGCCCAGGGTCCCTCTGTGCTTTTTCGCTTTCCTAAGCTCCTGTCGCTCCTCTTTGTCCCCTCAGTTTATGTCCTCCTGTGCTCACCTCCCTGACCTCTGTGACCTTGCACTCCCCTGGCCTGAAGCTGCCTCTCTGCGCGCTTTCTACTGGGCTCGTCTCTTTCCGGAGCCCCAGCGTCTCCTGCCCA
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_023067.4(FOXL2):c.673_*315inv variant causes a coding sequence, 3 prime UTR change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Consequence
FOXL2
NM_023067.4 coding_sequence, 3_prime_UTR
NM_023067.4 coding_sequence, 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.90
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 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-138945277-TGGGCAGGAGACGCTGGGGCTCCGGAAAGAGACGAGCCCAGTAGAAAGCGCGCAGAGAGGCAGCTTCAGGCCAGGGGAGTGCAAGGTCACAGAGGTCAGGGAGGTGAGCACAGGAGGACATAAACTGAGGGGACAAAGAGGAGCGACAGGAGCTTAGGAAAGCGAAAAAGCACAGAGGGACCCTGGGCGCTGGCTCCAGAGGCGGGCCCAGAGGGTGTGAGGTCAGGCTGGCGGCGGCGTCGTCGGCTGCGACCGGGGCCGGCGTCGCGCGTCCCTGCATCCTCGCATCCGTCTGCACCGGCATGCGGTGGGCTCTCAGAGATCGAGGCGCGAATGCAGCGCGCCGGTCTTGCTGTCGTGGTCCCAGTAAGAGCAATGCATCATGGCGAGCTCGGGCTGCCGGGCACAAGCGAACTGCAGGCCCGGCGCACTGGTGGGCGCGGGCGCCGGGGGCGCGGCGGTGGCTGGGCTGGCAGGGCTGAGCTGGCCCGGCGGCGGCGCGGCGGCCCCGTGGTGCGGTGGGGCAGGCGGCGGTGCGGCGGCCGCGTGCAGATGGTGTGCGTGCGGATGCGGGTGGGGGTGCGGCGGAGGCGGGGGTGCGGCCGGCGGGCCTCCCAGGCCATTGTACGAGTTCACTACGCCGGGGGGCAGCGCCATGCTCTGCACGCGTGTGTACGGCCCGTACGAGGCGGCCGGGCCCGCCAGCCCCTTGACCACAGCGGCCGCGCCAGGGCTACCGGGGCCCGCGGCTGCAGCCGCAGCTGCTGCAGCCGC-GCGGCTGCAGCAGCTGCGGCTGCAGCCGCGGGCCCCGGTAGCCCTGGCGCGGCCGCTGTGGTCAAGGGGCTGGCGGGCCCGGCCGCCTCGTACGGGCCGTACACACGCGTGCAGAGCATGGCGCTGCCCCCCGGCGTAGTGAACTCGTACAATGGCCTGGGAGGCCCGCCGGCCGCACCCCCGCCTCCGCCGCACCCCCACCCGCATCCGCACGCACACCATCTGCACGCGGCCGCCGCACCGCCGCCTGCCCCACCGCACCACGGGGCCGCCGCGCCGCCGCCGGGCCAGCTCAGCCCTGCCAGCCCAGCCACCGCCGCGCCCCCGGCGCCCGCGCCCACCAGTGCGCCGGGCCTGCAGTTCGCTTGTGCCCGGCAGCCCGAGCTCGCCATGATGCATTGCTCTTACTGGGACCACGACAGCAAGACCGGCGCGCTGCATTCGCGCCTCGATCTCTGAGAGCCCACCGCATGCCGGTGCAGACGGATGCGAGGATGCAGGGACGCGCGACGCCGGCCCCGGTCGCAGCCGACGACGCCGCCGCCAGCCTGACCTCACACCCTCTGGGCCCGCCTCTGGAGCCAGCGCCCAGGGTCCCTCTGTGCTTTTTCGCTTTCCTAAGCTCCTGTCGCTCCTCTTTGTCCCCTCAGTTTATGTCCTCCTGTGCTCACCTCCCTGACCTCTGTGACCTTGCACTCCCCTGGCCTGAAGCTGCCTCTCTGCGCGCTTTCTACTGGGCTCGTCTCTTTCCGGAGCCCCAGCGTCTCCTGCCCA is Pathogenic according to our data. Variant chr3-138945277-TGGGCAGGAGACGCTGGGGCTCCGGAAAGAGACGAGCCCAGTAGAAAGCGCGCAGAGAGGCAGCTTCAGGCCAGGGGAGTGCAAGGTCACAGAGGTCAGGGAGGTGAGCACAGGAGGACATAAACTGAGGGGACAAAGAGGAGCGACAGGAGCTTAGGAAAGCGAAAAAGCACAGAGGGACCCTGGGCGCTGGCTCCAGAGGCGGGCCCAGAGGGTGTGAGGTCAGGCTGGCGGCGGCGTCGTCGGCTGCGACCGGGGCCGGCGTCGCGCGTCCCTGCATCCTCGCATCCGTCTGCACCGGCATGCGGTGGGCTCTCAGAGATCGAGGCGCGAATGCAGCGCGCCGGTCTTGCTGTCGTGGTCCCAGTAAGAGCAATGCATCATGGCGAGCTCGGGCTGCCGGGCACAAGCGAACTGCAGGCCCGGCGCACTGGTGGGCGCGGGCGCCGGGGGCGCGGCGGTGGCTGGGCTGGCAGGGCTGAGCTGGCCCGGCGGCGGCGCGGCGGCCCCGTGGTGCGGTGGGGCAGGCGGCGGTGCGGCGGCCGCGTGCAGATGGTGTGCGTGCGGATGCGGGTGGGGGTGCGGCGGAGGCGGGGGTGCGGCCGGCGGGCCTCCCAGGCCATTGTACGAGTTCACTACGCCGGGGGGCAGCGCCATGCTCTGCACGCGTGTGTACGGCCCGTACGAGGCGGCCGGGCCCGCCAGCCCCTTGACCACAGCGGCCGCGCCAGGGCTACCGGGGCCCGCGGCTGCAGCCGCAGCTGCTGCAGCCGC-GCGGCTGCAGCAGCTGCGGCTGCAGCCGCGGGCCCCGGTAGCCCTGGCGCGGCCGCTGTGGTCAAGGGGCTGGCGGGCCCGGCCGCCTCGTACGGGCCGTACACACGCGTGCAGAGCATGGCGCTGCCCCCCGGCGTAGTGAACTCGTACAATGGCCTGGGAGGCCCGCCGGCCGCACCCCCGCCTCCGCCGCACCCCCACCCGCATCCGCACGCACACCATCTGCACGCGGCCGCCGCACCGCCGCCTGCCCCACCGCACCACGGGGCCGCCGCGCCGCCGCCGGGCCAGCTCAGCCCTGCCAGCCCAGCCACCGCCGCGCCCCCGGCGCCCGCGCCCACCAGTGCGCCGGGCCTGCAGTTCGCTTGTGCCCGGCAGCCCGAGCTCGCCATGATGCATTGCTCTTACTGGGACCACGACAGCAAGACCGGCGCGCTGCATTCGCGCCTCGATCTCTGAGAGCCCACCGCATGCCGGTGCAGACGGATGCGAGGATGCAGGGACGCGCGACGCCGGCCCCGGTCGCAGCCGACGACGCCGCCGCCAGCCTGACCTCACACCCTCTGGGCCCGCCTCTGGAGCCAGCGCCCAGGGTCCCTCTGTGCTTTTTCGCTTTCCTAAGCTCCTGTCGCTCCTCTTTGTCCCCTCAGTTTATGTCCTCCTGTGCTCACCTCCCTGACCTCTGTGACCTTGCACTCCCCTGGCCTGAAGCTGCCTCTCTGCGCGCTTTCTACTGGGCTCGTCTCTTTCCGGAGCCCCAGCGTCTCCTGCCCA is described in ClinVar as [Pathogenic]. Clinvar id is 1701464.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FOXL2 | NM_023067.4 | c.673_*315inv | coding_sequence_variant, 3_prime_UTR_variant | 1/1 | ENST00000648323.1 | NP_075555.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FOXL2 | ENST00000648323.1 | c.673_*315inv | coding_sequence_variant, 3_prime_UTR_variant | 1/1 | NM_023067.4 | ENSP00000497217 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.