chr13-102789185-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_024089.3(POGLUT2):c.1120G>A(p.Ala374Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,028 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 Uncertain significance (★).
Frequency
Consequence
NM_024089.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POGLUT2 | NM_024089.3 | c.1120G>A | p.Ala374Thr | missense_variant | Exon 7 of 10 | ENST00000376004.5 | NP_076994.2 | |
POGLUT2 | NM_001318732.2 | c.463G>A | p.Ala155Thr | missense_variant | Exon 8 of 11 | NP_001305661.1 | ||
POGLUT2 | XM_005254075.4 | c.1120G>A | p.Ala374Thr | missense_variant | Exon 7 of 9 | XP_005254132.1 | ||
POGLUT2 | XM_047430604.1 | c.463G>A | p.Ala155Thr | missense_variant | Exon 5 of 8 | XP_047286560.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251310Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135814
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727234
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1120G>A (p.A374T) alteration is located in exon 7 (coding exon 7) of the KDELC1 gene. This alteration results from a G to A substitution at nucleotide position 1120, causing the alanine (A) at amino acid position 374 to be replaced by a threonine (T). 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