7-38726932-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014396.4(VPS41):c.2461G>A(p.Glu821Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014396.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS41 | NM_014396.4 | c.2461G>A | p.Glu821Lys | missense_variant | Exon 28 of 29 | ENST00000310301.9 | NP_055211.2 | |
VPS41 | NM_080631.4 | c.2386G>A | p.Glu796Lys | missense_variant | Exon 27 of 28 | NP_542198.2 | ||
VPS41 | XM_017011988.2 | c.1306G>A | p.Glu436Lys | missense_variant | Exon 15 of 16 | XP_016867477.1 | ||
VPS41 | XR_007060008.1 | n.2572G>A | non_coding_transcript_exon_variant | Exon 29 of 29 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2461G>A (p.E821K) alteration is located in exon 28 (coding exon 28) of the VPS41 gene. This alteration results from a G to A substitution at nucleotide position 2461, causing the glutamic acid (E) at amino acid position 821 to be replaced by a lysine (K). 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.