10-102230682-CGCGGCGGCG-CGCG
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP3BS2
The NM_005029.4(PITX3):c.735_740delCGCCGC(p.Ala246_Ala247del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000351 in 1,426,408 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Consequence
PITX3
NM_005029.4 disruptive_inframe_deletion
NM_005029.4 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.42
Genes affected
PITX3 (HGNC:9006): (paired like homeodomain 3) This gene encodes a member of the RIEG/PITX homeobox family, which is in the bicoid class of homeodomain proteins. Members of this family act as transcription factors. This protein is involved in lens formation during eye development. Mutations of this gene have been associated with anterior segment mesenchymal dysgenesis and congenital cataracts. [provided by RefSeq, Jul 2008]
GBF1 (HGNC:4181): (golgi brefeldin A resistant guanine nucleotide exchange factor 1) This gene encodes a member of the Sec7 domain family. The encoded protein is a guanine nucleotide exchange factor that regulates the recruitment of proteins to membranes by mediating GDP to GTP exchange. The encoded protein is localized to the Golgi apparatus and plays a role in vesicular trafficking by activating ADP ribosylation factor 1. The encoded protein has also been identified as an important host factor for viral replication. Multiple transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_005029.4
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PITX3 | NM_005029.4 | c.735_740delCGCCGC | p.Ala246_Ala247del | disruptive_inframe_deletion | Exon 4 of 4 | ENST00000370002.8 | NP_005020.1 | |
| PITX3 | XM_047425352.1 | c.735_740delCGCCGC | p.Ala246_Ala247del | disruptive_inframe_deletion | Exon 3 of 3 | XP_047281308.1 | ||
| GBF1 | NM_001391923.1 | c.-233_-228delGGCGGC | 5_prime_UTR_variant | Exon 1 of 40 | NP_001378852.1 | |||
| GBF1 | NM_001391924.1 | c.-371_-366delGGCGGC | 5_prime_UTR_variant | Exon 1 of 41 | NP_001378853.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000351 AC: 5AN: 1426408Hom.: 0 AF XY: 0.00000425 AC XY: 3AN XY: 706706
GnomAD4 exome
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5
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1426408
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3
AN XY:
706706
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at