rs387906472
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_ModeratePP5_Very_Strong
The NM_000032.5(ALAS2):c.1706_1709del(p.Glu569GlyfsTer24) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 22)
Consequence
ALAS2
NM_000032.5 frameshift
NM_000032.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
ALAS2 (HGNC:397): (5'-aminolevulinate synthase 2) The product of this gene specifies an erythroid-specific mitochondrially located enzyme. The encoded protein catalyzes the first step in the heme biosynthetic pathway. Defects in this gene cause X-linked pyridoxine-responsive sideroblastic anemia. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0329 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
PP5
?
Variant X-55009234-CCACT-C is Pathogenic according to our data. Variant chrX-55009234-CCACT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10482.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALAS2 | NM_000032.5 | c.1706_1709del | p.Glu569GlyfsTer24 | frameshift_variant | 11/11 | ENST00000650242.1 | |
ALAS2 | NM_001037967.4 | c.1595_1598del | p.Glu532GlyfsTer24 | frameshift_variant | 10/10 | ||
ALAS2 | NM_001037968.4 | c.1667_1670del | p.Glu556GlyfsTer24 | frameshift_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALAS2 | ENST00000650242.1 | c.1706_1709del | p.Glu569GlyfsTer24 | frameshift_variant | 11/11 | NM_000032.5 | P1 | ||
ALAS2 | ENST00000335854.8 | c.1595_1598del | p.Glu532GlyfsTer24 | frameshift_variant | 10/10 | 2 | |||
ALAS2 | ENST00000396198.7 | c.1667_1670del | p.Glu556GlyfsTer24 | frameshift_variant | 11/11 | 5 | |||
ALAS2 | ENST00000498636.1 | c.*4_*7del | 3_prime_UTR_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:3Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
X-linked erythropoietic protoporphyria Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2013 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2023 | For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this frameshift affects ALAS2 function (PMID: 23263862). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 10482). This frameshift has been observed in individual(s) with X-linked dominant erythropoietic protoporphyria (PMID: 18760763). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the ALAS2 gene (p.Glu569Glyfs*24). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 19 amino acid(s) of the ALAS2 protein and extend the protein by 4 additional amino acid residues. - |
Erythema Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University Hospital Muenster | Dec 20, 2021 | ACMG categories: PVS1,PM2 - |
Computational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at