rs1553752849

Variant names:

• chr3-138946022-G-GGCGGCTGCAGCCGCAGCTGCTGCAGCCGCT
• rs1553752849
• NM_023067.4:c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PP5_Moderate BP3

The NM_023067.4(FOXL2):​c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC​(p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: FOXL2 NM_023067.4 conservative_inframe_insertion
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.32
• Publications: 0 publications found

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]

FOXL2 Gene-Disease associations (from GenCC):

• blepharophimosis, ptosis, and epicanthus inversus syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• premature ovarian failure 3

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP5: Variant 3-138946022-G-GGCGGCTGCAGCCGCAGCTGCTGCAGCCGCT is Pathogenic according to our data. Variant chr3-138946022-G-GGCGGCTGCAGCCGCAGCTGCTGCAGCCGCT is described in ClinVar as Pathogenic. ClinVar VariationId is 559900.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP3: Nonframeshift variant in repetitive region in NM_023067.4

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_023067.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXL2	NM_023067.4	MANE Select	c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC	p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro	conservative_inframe_insertion	Exon 1 of 1	NP_075555.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FOXL2	ENST00000648323.1	MANE Select	c.700_701insAGCGGCTGCAGCAGCTGCGGCTGCAGCCGC	p.Ala234delinsGluArgLeuGlnGlnLeuArgLeuGlnProPro	conservative_inframe_insertion	Exon 1 of 1	ENSP00000497217.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Blepharophimosis, ptosis, and epicanthus inversus syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.3
Mutation Taster		=40/160	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1553752849; hg19: chr3-138664864;