rs104894674
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_203486.3(DLL3):c.1154G>A(p.Gly385Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000359 in 1,391,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_203486.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLL3 | NM_203486.3 | c.1154G>A | p.Gly385Asp | missense_variant | 7/9 | ENST00000356433.10 | |
DLL3 | NM_016941.4 | c.1154G>A | p.Gly385Asp | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLL3 | ENST00000356433.10 | c.1154G>A | p.Gly385Asp | missense_variant | 7/9 | 2 | NM_203486.3 | P1 | |
DLL3 | ENST00000205143.4 | c.1154G>A | p.Gly385Asp | missense_variant | 7/8 | 1 | |||
DLL3 | ENST00000596614.5 | c.470G>A | p.Gly157Asp | missense_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000359 AC: 5AN: 1391250Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 687702
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Spondylocostal dysostosis 1, autosomal recessive Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at