15-52124617-G-C
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_016194.4(GNB5):āc.1032C>Gā(p.Tyr344*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,628 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 Pathogenic (ā ā ).
Frequency
Consequence
NM_016194.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNB5 | NM_016194.4 | c.1032C>G | p.Tyr344* | stop_gained | Exon 12 of 13 | ENST00000261837.12 | NP_057278.2 | |
GNB5 | NM_006578.4 | c.906C>G | p.Tyr302* | stop_gained | Exon 10 of 11 | NP_006569.1 | ||
GNB5 | NM_001379343.1 | c.750C>G | p.Tyr250* | stop_gained | Exon 10 of 11 | NP_001366272.1 | ||
GNB5 | XM_011521162.4 | c.906C>G | p.Tyr302* | stop_gained | Exon 10 of 11 | XP_011519464.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251104Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135694
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461628Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727110
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:3
For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in GNB5 are known to be pathogenic (PMID: 21766168, 27523599). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has been observed in individual(s) with GNB5-related conditions (PMID: 27523599). ClinVar contains an entry for this variant (Variation ID: 268102). This variant is present in population databases (rs749597091, ExAC 0.006%). This sequence change creates a premature translational stop signal (p.Tyr344*) in the GNB5 gene. It is expected to result in an absent or disrupted protein product. -
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Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32280589, 31631344, 31720979, 32477400, 28327206, 33172956, 32203251, 27523599) -
Gnb5-related intellectual disability-cardiac arrhythmia syndrome Pathogenic:2Other:1
Recurrent variant reported in 6 families from India and Pakistan -
This variant was identified as compound heterozygous in an individual with devleopmental delay, intellectual disability, hypotonia, retinal dystrophy, arrhythmia. -
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Inborn genetic diseases Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at