2-236166192-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001485.4(GBX2):c.769G>A(p.Glu257Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001485.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GBX2 | NM_001485.4 | c.769G>A | p.Glu257Lys | missense_variant | Exon 2 of 2 | ENST00000306318.5 | NP_001476.2 | |
GBX2 | XM_047443907.1 | c.769G>A | p.Glu257Lys | missense_variant | Exon 2 of 4 | XP_047299863.1 | ||
GBX2 | NM_001301687.2 | c.*137G>A | 3_prime_UTR_variant | Exon 3 of 3 | NP_001288616.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBX2 | ENST00000306318.5 | c.769G>A | p.Glu257Lys | missense_variant | Exon 2 of 2 | 1 | NM_001485.4 | ENSP00000302251.4 | ||
GBX2 | ENST00000551105 | c.*137G>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000448747.1 | ||||
GBX2 | ENST00000465889.1 | n.438G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250580Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135684
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461598Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727110
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.769G>A (p.E257K) alteration is located in exon 2 (coding exon 2) of the GBX2 gene. This alteration results from a G to A substitution at nucleotide position 769, causing the glutamic acid (E) at amino acid position 257 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at