11-65348869-A-G
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Moderate
The NM_006268.5(DPF2):c.1037A>G(p.Asp346Gly) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D346N) has been classified as Likely pathogenic.
Frequency
Consequence
NM_006268.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPF2 | NM_006268.5 | c.1037A>G | p.Asp346Gly | missense_variant | 10/11 | ENST00000528416.6 | |
DPF2 | NM_001330308.2 | c.1079A>G | p.Asp360Gly | missense_variant | 11/12 | ||
DPF2 | XM_017018101.3 | c.1019A>G | p.Asp340Gly | missense_variant | 11/12 | ||
DPF2 | XR_007062491.1 | n.993A>G | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPF2 | ENST00000528416.6 | c.1037A>G | p.Asp346Gly | missense_variant | 10/11 | 1 | NM_006268.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Coffin-Siris syndrome 7 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics Lab, CHRU Brest | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 28, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at