rs104886376
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PS1_ModeratePP5
The NM_033380.3(COL4A5):c.2_3del(p.Met1?) variant causes a frameshift, start lost change. Variant has been reported in Lovd as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 20)
Consequence
COL4A5
NM_033380.3 frameshift, start_lost
NM_033380.3 frameshift, start_lost
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.04
Genes affected
COL4A5 (HGNC:2207): (collagen type IV alpha 5 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 840 pathogenic variants in the truncated region.
PS1
?
Another start lost variant in NM_033380.3 (COL4A5) was described as [Pathogenic] in ClinVar as 24214
PP5
?
Variant X-108440126-ATG-A is Pathogenic according to our data. Variant chrX-108440126-ATG-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.2_3del | p.Met1? | frameshift_variant, start_lost | 1/53 | ENST00000328300.11 | |
COL4A5 | NM_000495.5 | c.2_3del | p.Met1? | frameshift_variant, start_lost | 1/51 | ||
COL4A5 | XM_047441811.1 | c.2_3del | p.Met1? | frameshift_variant, start_lost | 1/42 | ||
COL4A5 | XM_047441810.1 | c.-375_-374del | 5_prime_UTR_variant | 1/54 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.2_3del | p.Met1? | frameshift_variant, start_lost | 1/53 | 1 | NM_033380.3 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD3 genomes
?
Cov.:
20
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 20
GnomAD4 genome
?
Cov.:
20
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at