rs1554709553
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP3
The NM_005458.8(GABBR2):c.954_959delTTTCGA(p.Asp318_Phe319del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005458.8 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.954_959delTTTCGA | p.Asp318_Phe319del | disruptive_inframe_deletion | Exon 6 of 19 | ENST00000259455.4 | NP_005449.5 | |
GABBR2 | XM_017015331.3 | c.660_665delTTTCGA | p.Asp220_Phe221del | disruptive_inframe_deletion | Exon 5 of 18 | XP_016870820.1 | ||
GABBR2 | XM_005252316.6 | c.180_185delTTTCGA | p.Asp60_Phe61del | disruptive_inframe_deletion | Exon 4 of 17 | XP_005252373.1 | ||
GABBR2 | XM_017015332.3 | c.180_185delTTTCGA | p.Asp60_Phe61del | disruptive_inframe_deletion | Exon 3 of 16 | XP_016870821.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.954_959delTTTCGA | p.Asp318_Phe319del | disruptive_inframe_deletion | Exon 6 of 19 | 1 | NM_005458.8 | ENSP00000259455.2 | ||
GABBR2 | ENST00000634919.1 | n.732_737delTTTCGA | non_coding_transcript_exon_variant | Exon 5 of 6 | 5 | |||||
GABBR2 | ENST00000637410.1 | n.732_737delTTTCGA | non_coding_transcript_exon_variant | Exon 6 of 19 | 5 | |||||
GABBR2 | ENST00000477471.1 | n.*39_*44delTTTCGA | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Epileptic encephalopathy Uncertain:1
Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. This variant has not been reported in the literature in individuals with a GABBR2-related disease. This variant is not present in population databases (ExAC no frequency). This variant, c.954_959delTTTCGA, results in the deletion of 2 amino acids of the GABBR2 protein (p.Asp318_Phe319del), but otherwise preserves the integrity of the reading frame. In summary, this variant has uncertain impact on GABBR2 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at