rs1553234309
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_003126.4(SPTA1):c.1850_1851insA(p.Ser618GlufsTer10) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 31)
Consequence
SPTA1
NM_003126.4 frameshift
NM_003126.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.69
Genes affected
SPTA1 (HGNC:11272): (spectrin alpha, erythrocytic 1) This gene encodes a member of a family of molecular scaffold proteins that link the plasma membrane to the actin cytoskeleton and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. The encoded protein is primarily composed of 22 spectrin repeats which are involved in dimer formation. It forms a component of the erythrocyte plasma membrane. Mutations in this gene result in a variety of hereditary red blood cell disorders, including elliptocytosis-2, pyropoikilocytosis, and spherocytosis, type 3. [provided by RefSeq, Aug 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-158668045-C-CT is Pathogenic according to our data. Variant chr1-158668045-C-CT is described in ClinVar as [Pathogenic]. Clinvar id is 496724.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPTA1 | NM_003126.4 | c.1850_1851insA | p.Ser618GlufsTer10 | frameshift_variant | 15/52 | ENST00000643759.2 | NP_003117.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPTA1 | ENST00000643759.2 | c.1850_1851insA | p.Ser618GlufsTer10 | frameshift_variant | 15/52 | NM_003126.4 | ENSP00000495214 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary spherocytosis type 3 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | MVZ Dr. Eberhard & Partner Dortmund | Jan 02, 2018 | Frameshift mutation that generates a premature stop at codon 627 which is predicted to result in a shortend unfunctional protein or NMD, p.(Ser618Glufs*10). LOF is a known mechanism in SPTA1. NM_003126.2 c.1850dup was observed with the pathogenic variant NM_003126.2 c.4339-99C>T (IVS30-99C>T) in an individual with indication for Spherocytosis type 3. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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