rs1553234309

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

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 5.69
Variant links:
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]

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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
SPTA1NM_003126.4 linkuse as main transcriptc.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
SPTA1ENST00000643759.2 linkuse as main transcriptc.1850_1851insA p.Ser618GlufsTer10 frameshift_variant 15/52 NM_003126.4 ENSP00000495214 P1P02549-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
32
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 submitterclinical testingMVZ Dr. Eberhard & Partner DortmundJan 02, 2018Frameshift 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1553234309; hg19: chr1-158637835; API