7-76302715-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001540.5(HSPB1):c.3G>A(p.Met1?) variant causes a start lost change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000025 in 1,601,518 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001540.5 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 33
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1449302Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 721464
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
The p.M1? variant (also known as c.3G>A) is located in coding exon 1 of the HSPB1 gene and results from a G to A substitution at nucleotide position 3. This alters the methionine residue at the initiation codon. There is an in-frame methionine 169 amino acids downstream from this initiation site which, if used, may result in an N-terminal truncation impacting the alpha-crystallin domain of HSPB1 which is thought to be crucial for the overall structure of small heat shock proteins; however, direct evidence is unavailable (Benndorf R et al. Mutat Res Rev Mutat Res 2014 pii: S1383-5742(14)00018-0). Since sequence variations that modify the initiation codon (ATG) are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame, this alteration is interpreted as likely pathogenic. -
Charcot-Marie-Tooth disease axonal type 2F Uncertain:1
This sequence change affects the initiator methionine of the HSPB1 mRNA. The next in-frame methionine is located at codon 169. This variant is present in population databases (no rsID available, gnomAD 0.0008%). This variant has not been reported in the literature in individuals affected with HSPB1-related conditions. ClinVar contains an entry for this variant (Variation ID: 934124). In summary, the available evidence is currently insufficient to determine the role of this variant 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