rs104886224
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2PM5PP3_StrongPP5_Very_Strong
The NM_033380.3(COL4A5):c.3311G>A(p.Gly1104Asp) 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1104R) has been classified as Pathogenic.
Frequency
Consequence
NM_033380.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.3311G>A | p.Gly1104Asp | missense_variant | 37/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.3311G>A | p.Gly1104Asp | missense_variant | 37/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000361603.7 | c.3311G>A | p.Gly1104Asp | missense_variant | 37/51 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
X-linked Alport syndrome Pathogenic:2
Likely pathogenic, criteria provided, single submitter | research | Precision Medicine Center, Zhengzhou University | - | PM1:Located in a mutational hot spot PM2:not found in gnomAD PM5:Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before PP3:Multiple lines of computational evidence support a deleterious effect on the gene or gene product - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Suma Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.