rs121912755
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_000342.4(SLC4A1):c.2279G>A(p.Arg760Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,008 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 Likely pathogenic (★★).
Frequency
Consequence
NM_000342.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC4A1 | NM_000342.4 | c.2279G>A | p.Arg760Gln | missense_variant | Exon 17 of 20 | ENST00000262418.12 | NP_000333.1 | |
SLC4A1 | XM_011525129.3 | c.2189G>A | p.Arg730Gln | missense_variant | Exon 16 of 19 | XP_011523431.1 | ||
SLC4A1 | XM_005257593.6 | c.2084G>A | p.Arg695Gln | missense_variant | Exon 15 of 18 | XP_005257650.1 | ||
SLC4A1 | XM_011525130.2 | c.2279G>A | p.Arg760Gln | missense_variant | Exon 17 of 18 | XP_011523432.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC4A1 | ENST00000262418.12 | c.2279G>A | p.Arg760Gln | missense_variant | Exon 17 of 20 | 1 | NM_000342.4 | ENSP00000262418.6 | ||
SLC4A1 | ENST00000399246.3 | c.1181G>A | p.Arg394Gln | missense_variant | Exon 12 of 15 | 5 | ENSP00000382190.3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461008Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726810
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Pathogenic:3
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 760 of the SLC4A1 protein (p.Arg760Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with spherocytosis (PMID: 7530501, 32641076). ClinVar contains an entry for this variant (Variation ID: 17780). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC4A1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects SLC4A1 function (PMID: 11208088, 23842529). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -
- -
The SLC4A1 c.2279G>A; p.Arg760Gln variant (rs121912755), also known as Band 3 Prague II, is reported in the literature in individuals affected with hereditary spherocytosis (Bruce 2005, Fermo 2021, Jarolim 1995, Van Zwieten 2013, Vercellati 2022, Yawata 2001). This variant is also reported in ClinVar (Variation ID: 17780). Functional analyses show that the variant protein is not incorporated into the cell membrane of erythrocytes and is associated with abnormal membrane permeability and ion fluxes (Bruce 2005, Jarolim 1995, Quilty 2000). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.898). Based on available information, this variant is considered to be likely pathogenic. REFERENCES Bruce LJ et al. Monovalent cation leaks in human red cells caused by single amino-acid substitutions in the transport domain of the band 3 chloride-bicarbonate exchanger, AE1. Nature genetics. 2005 Nov. PMID: 16227998 Fermo E et al. Targeted Next Generation Sequencing and Diagnosis of Congenital Hemolytic Anemias: A Three Years Experience Monocentric Study. Front Physiol. 2021 PMID: 34093240 Jarolim P et al. Mutations of conserved arginines in the membrane domain of erythroid band 3 lead to a decrease in membrane-associated band 3 and to the phenotype of hereditary spherocytosis. Blood. 1995 Feb 1. PMID: 7530501 Quilty JA et al. Trafficking and folding defects in hereditary spherocytosis mutants of the human red cell anion exchanger. Traffic. 2000 Dec. PMID: 11208088 Van Zwieten R et al. Hereditary spherocytosis due to band 3 deficiency: 15 novel mutations in SLC4A1. Am J Hematol. 2013 Feb. PMID: 23255290 Vercellati C et al. Effect of primary lesions in cytoskeleton proteins on red cell membrane stability in patients with hereditary spherocytosis. Front Physiol. 2022 PMID: 36035481 Yawata Y et al. Hereditary Red Cell Membrane Disorders in Japan: Their Genotypic and Phenotypic Features in 1014 Cases Studied. Hematology. 2001 PMID: 27405697 -
Hereditary spherocytosis type 4 Pathogenic:2
Criteria applied: PS4_MOD,PM1,PM5,PM2_SUP,PP2,PP3,PP4 -
- -
BLOOD GROUP--DIEGO SYSTEM;C1832168:BLOOD GROUP--FROESE;C1832169:BLOOD GROUP--SWANN SYSTEM;C1861453:Cryohydrocytosis;C1862190:BLOOD GROUP--WRIGHT ANTIGEN;C1862191:BLOOD GROUP--WALDNER TYPE;C1862322:Southeast Asian ovalocytosis;C1970028:Malaria, susceptibility to;C2675212:Hereditary spherocytosis type 4;C5436235:Renal tubular acidosis, distal, 4, with hemolytic anemia;CN280572:Autosomal dominant distal renal tubular acidosis Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at