rs1003232768
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The ENST00000675609.1(GJB1):c.-165-8T>C variant causes a splice region, splice polypyrimidine tract, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 22)
Consequence
GJB1
ENST00000675609.1 splice_region, splice_polypyrimidine_tract, intron
ENST00000675609.1 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.67
Genes affected
GJB1 (HGNC:4283): (gap junction protein beta 1) This gene encodes a member of the gap junction protein family. The gap junction proteins are membrane-spanning proteins that assemble to form gap junction channels that facilitate the transfer of ions and small molecules between cells. According to sequence similarities at the nucleotide and amino acid levels, the gap junction proteins are divided into two categories, alpha and beta. Mutations in this gene cause X-linked Charcot-Marie-Tooth disease, an inherited peripheral neuropathy. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-71223179-T-C is Pathogenic according to our data. Variant chrX-71223179-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 543921.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Uncertain_significance=1}. Variant chrX-71223179-T-C is described in Lovd as [Pathogenic].
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJB1 | NM_001097642.3 | c.-16-513T>C | intron_variant | ||||
GJB1 | XM_011530907.3 | c.-17+413T>C | intron_variant | ||||
GJB1 | NM_000166.6 | upstream_gene_variant | ENST00000361726.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJB1 | ENST00000361726.7 | upstream_gene_variant | 1 | NM_000166.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Charcot-Marie-Tooth Neuropathy X Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | This variant occurs in a non-coding region of the GJB1 gene. It does not change the encoded amino acid sequence of the GJB1 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant has been observed in individuals with Charcot-Marie-Tooth disease (PMID: 16373087, 21918739, 23827825; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as c.-529T>C. ClinVar contains an entry for this variant (Variation ID: 543921). Studies have shown that this variant alters GJB1 gene expression (PMID: 23827825). For these reasons, this variant has been classified as Pathogenic. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2023 | Reported previously in a patient with a clinical diagnosis of CMT including slowly progressive weakness, atrophy of distal limb muscles, numbness over feet, generalized areflexia, and mild sensory loss over feet (Tsai et al., 2013); Reported previously in an affected male and female patient and three unaffected female patients in one family with a diagnosis of CMT (Beauvais et al., 2006); Published function studies show that this variant does not significantly alter luciferase activity (Tsai et al., 2013); No data available from control populations to assess the frequency of this variant; Also known as c.-529T>C; This variant is associated with the following publications: (PMID: 31211173, 16373087, 23827825) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at