chr7-140527472-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015689.5(DENND2A):c.2351C>A(p.Ala784Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. A784T) has been classified as Uncertain significance.
Frequency
Consequence
NM_015689.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DENND2A | NM_015689.5 | c.2351C>A | p.Ala784Glu | missense_variant | 15/20 | ENST00000496613.6 | |
DENND2A | NM_001318052.2 | c.2351C>A | p.Ala784Glu | missense_variant | 14/19 | ||
DENND2A | NM_001362678.2 | c.2351C>A | p.Ala784Glu | missense_variant | 15/20 | ||
DENND2A | NR_134477.1 | n.2473-35C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DENND2A | ENST00000496613.6 | c.2351C>A | p.Ala784Glu | missense_variant | 15/20 | 2 | NM_015689.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.2351C>A (p.A784E) alteration is located in exon 13 (coding exon 13) of the DENND2A gene. This alteration results from a C to A substitution at nucleotide position 2351, causing the alanine (A) at amino acid position 784 to be replaced by a glutamic acid (E). 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.