rs121434255
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_000383.4(AIRE):āc.247A>Gā(p.Lys83Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,460,770 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. K83K) has been classified as Likely benign.
Frequency
Consequence
NM_000383.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIRE | NM_000383.4 | c.247A>G | p.Lys83Glu | missense_variant | 2/14 | ENST00000291582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIRE | ENST00000291582.6 | c.247A>G | p.Lys83Glu | missense_variant | 2/14 | 1 | NM_000383.4 | P1 | |
AIRE | ENST00000527919.5 | n.408A>G | non_coding_transcript_exon_variant | 2/14 | 2 | ||||
AIRE | ENST00000530812.5 | n.416A>G | non_coding_transcript_exon_variant | 2/12 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460770Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 726706
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Polyglandular autoimmune syndrome, type 1 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2022 | 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. Experimental studies have shown that this missense change affects AIRE function (PMID: 14974083). 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 AIRE protein function. ClinVar contains an entry for this variant (Variation ID: 3308). This missense change has been observed in individual(s) with autosomal recessive autoimmune polyendocrinopathy syndrome (PMID: 9398839). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 83 of the AIRE protein (p.Lys83Glu). - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at