rs1555032051
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP2PP3PP5_Moderate
The NM_006268.5(DPF2):c.1049G>A(p.Arg350His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,886 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R350C) has been classified as Uncertain significance.
Frequency
Consequence
NM_006268.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPF2 | NM_006268.5 | c.1049G>A | p.Arg350His | missense_variant | 10/11 | ENST00000528416.6 | |
DPF2 | NM_001330308.2 | c.1091G>A | p.Arg364His | missense_variant | 11/12 | ||
DPF2 | XM_017018101.3 | c.1031G>A | p.Arg344His | missense_variant | 11/12 | ||
DPF2 | XR_007062491.1 | n.1005G>A | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPF2 | ENST00000528416.6 | c.1049G>A | p.Arg350His | missense_variant | 10/11 | 1 | NM_006268.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461886Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727244
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2019 | - - |
Coffin-Siris syndrome 7 Pathogenic:1
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