rs140973844
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001167.4(XIAP):c.683T>G(p.Phe228Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000014 in 1,210,357 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F228S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001167.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XIAP | NM_001167.4 | c.683T>G | p.Phe228Cys | missense_variant | 2/7 | ENST00000371199.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XIAP | ENST00000371199.8 | c.683T>G | p.Phe228Cys | missense_variant | 2/7 | 1 | NM_001167.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112095Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34271
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183502Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67940
GnomAD4 exome AF: 0.0000137 AC: 15AN: 1098262Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363616
GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112095Hom.: 0 Cov.: 23 AF XY: 0.0000292 AC XY: 1AN XY: 34271
ClinVar
Submissions by phenotype
X-linked lymphoproliferative disease due to XIAP deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 22, 2023 | This sequence change replaces phenylalanine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 228 of the XIAP protein (p.Phe228Cys). This variant is present in population databases (rs140973844, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with XIAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 571391). 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 not expected to disrupt XIAP protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at