chr1-228158476-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_020435.4(GJC2):c.718C>T(p.Arg240*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,772 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 (★).
Frequency
Consequence
NM_020435.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJC2 | NM_020435.4 | c.718C>T | p.Arg240* | stop_gained | Exon 2 of 2 | ENST00000366714.3 | NP_065168.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151904Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1459868Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 726332
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151904Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74198
ClinVar
Submissions by phenotype
Hypomyelinating leukodystrophy 2 Pathogenic:2
This mutation has been previously reported as disease-causing and was found once in our laboratory in trans with a pathogenic variant in a 4-year-old male with intellectual disability, hypotonia, spasticity, wide-based gait, significantly delayed myelination, nystagmus, cerebral palsy -
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not provided Pathogenic:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at