rs104894324
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The ENST00000229335.11(AICDA):c.70C>T(p.Arg24Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,860 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R24Q) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000229335.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AICDA | NM_020661.4 | c.70C>T | p.Arg24Trp | missense_variant | 2/5 | ENST00000229335.11 | NP_065712.1 | |
AICDA | NM_001330343.2 | c.70C>T | p.Arg24Trp | missense_variant | 2/5 | NP_001317272.1 | ||
AICDA | NM_001410970.1 | c.70C>T | p.Arg24Trp | missense_variant | 2/4 | NP_001397899.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AICDA | ENST00000229335.11 | c.70C>T | p.Arg24Trp | missense_variant | 2/5 | 1 | NM_020661.4 | ENSP00000229335 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249542Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135392
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461860Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727230
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hyper-IgM syndrome type 2 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 16, 2023 | ClinVar contains an entry for this variant (Variation ID: 5122). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg24 amino acid residue in AICDA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27577878; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects AICDA function (PMID: 22715099). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This missense change has been observed in individuals with autosomal recessive hyper Ig M syndrome (PMID: 11007475, 26551569). This variant is present in population databases (rs104894324, gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 24 of the AICDA protein (p.Arg24Trp). - |
Pathogenic, criteria provided, single submitter | clinical testing | 3billion | Jan 03, 2022 | Same nucleotide change resulting in same amino acid change has been previously reported to be associated with AICDA related disorder (ClinVar ID: VCV000005122, PMID:11007475, PS1). The variant has been observed in multiple (>3) similarly affected unrelated individuals(PMID: 11007475, PS4_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.869, 3CNET: 0.925, PP3_P). A missense variant is a common mechanism associated with Immunodeficiency with hyper-IgM (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000004, PM2_M). A different missense change at the same codon has been reported to be associated with AICDA related disorder (PMID:27577878, PM5_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at