3-138945277-TGGGCAGGAGACGCTGGGGCTCCGGAAAGAGACGAGCCCAGTAGAAAGCGCGCAGAGAGGCAGCTTCAGGCCAGGGGAGTGCAAGGTCACAGAGGTCAGGGAGGTGAGCACAGGAGGACATAAACTGAGGGGACAAAGAGGAGCGACAGGAGCTTAGGAAAGCGAAAAAGCACAGAGGGACCCTGGGCGCTGGCTCCAGAGGCGGGCCCAGAGGGTGTGAGGTCAGGCTGGCGGCGGCGTCGTCGGCTGCGACCGGGGCCGGCGTCGCGCGTCCCTGCATCCTCGCATCCGTCTGCACCGGCATGCGGTGGGCTCTCAGAGATCGAGGCGCGAATGCAGCGCGCCGGTCTTGCTGTCGTGGTCCCAGTAAGAGCAATGCATCATGGCGAGCTCGGGCTGCCGGGCACAAGCGAACTGCAGGCCCGGCGCACTGGTGGGCGCGGGCGCCGGGGGCGCGGCGGTGGCTGGGCTGGCAGGGCTGAGCTGGCCCGGCGGCGGCGCGGCGGCCCCGTGGTGCGGTGGGGCAGGCGGCGGTGCGGCGGCCGCGTGCAGATGGTGTGCGTGCGGATGCGGGTGGGGGTGCGGCGGAGGCGGGGGTGCGGCCGGCGGGCCTCCCAGGCCATTGTACGAGTTCACTACGCCGGGGGGCAGCGCCATGCTCTGCACGCGTGTGTACGGCCCGTACGAGGCGGCCGGGCCCGCCAGCCCCTTGACCACAGCGGCCGCGCCAGGGCTACCGGGGCCCGCGGCTGCAGCCGCAGCTGCTGCAGCCGC-GCGGCTGCAGCAGCTGCGGCTGCAGCCGCGGGCCCCGGTAGCCCTGGCGCGGCCGCTGTGGTCAAGGGGCTGGCGGGCCCGGCCGCCTCGTACGGGCCGTACACACGCGTGCAGAGCATGGCGCTGCCCCCCGGCGTAGTGAACTCGTACAATGGCCTGGGAGGCCCGCCGGCCGCACCCCCGCCTCCGCCGCACCCCCACCCGCATCCGCACGCACACCATCTGCACGCGGCCGCCGCACCGCCGCCTGCCCCACCGCACCACGGGGCCGCCGCGCCGCCGCCGGGCCAGCTCAGCCCTGCCAGCCCAGCCACCGCCGCGCCCCCGGCGCCCGCGCCCACCAGTGCGCCGGGCCTGCAGTTCGCTTGTGCCCGGCAGCCCGAGCTCGCCATGATGCATTGCTCTTACTGGGACCACGACAGCAAGACCGGCGCGCTGCATTCGCGCCTCGATCTCTGAGAGCCCACCGCATGCCGGTGCAGACGGATGCGAGGATGCAGGGACGCGCGACGCCGGCCCCGGTCGCAGCCGACGACGCCGCCGCCAGCCTGACCTCACACCCTCTGGGCCCGCCTCTGGAGCCAGCGCCCAGGGTCCCTCTGTGCTTTTTCGCTTTCCTAAGCTCCTGTCGCTCCTCTTTGTCCCCTCAGTTTATGTCCTCCTGTGCTCACCTCCCTGACCTCTGTGACCTTGCACTCCCCTGGCCTGAAGCTGCCTCTCTGCGCGCTTTCTACTGGGCTCGTCTCTTTCCGGAGCCCCAGCGTCTCCTGCCCA

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_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
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• 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]

ACMG classification

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	UniProt
FOXL2	NM_023067.4	c.673_*315inv		coding_sequence_variant, 3_prime_UTR_variant	1/1	ENST00000648323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXL2	ENST00000648323.1	c.673_*315inv		coding_sequence_variant, 3_prime_UTR_variant	1/1		NM_023067.4	P1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

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: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-138664119;