NM_024089.3:c.1223A>G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024089.3(POGLUT2):c.1223A>G(p.Tyr408Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000028 in 1,461,838 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024089.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POGLUT2 | NM_024089.3 | c.1223A>G | p.Tyr408Cys | missense_variant | Exon 7 of 10 | ENST00000376004.5 | NP_076994.2 | |
POGLUT2 | NM_001318732.2 | c.566A>G | p.Tyr189Cys | missense_variant | Exon 8 of 11 | NP_001305661.1 | ||
POGLUT2 | XM_005254075.4 | c.1223A>G | p.Tyr408Cys | missense_variant | Exon 7 of 9 | XP_005254132.1 | ||
POGLUT2 | XM_047430604.1 | c.566A>G | p.Tyr189Cys | missense_variant | Exon 5 of 8 | XP_047286560.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461838Hom.: 1 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727234
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1223A>G (p.Y408C) alteration is located in exon 7 (coding exon 7) of the KDELC1 gene. This alteration results from a A to G substitution at nucleotide position 1223, causing the tyrosine (Y) at amino acid position 408 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.