rs104886353
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM4PP5
The NM_033380.3(COL4A5):c.2411_2428del(p.Asn804_Pro809del) variant causes a inframe deletion change. Variant has been reported in Lovd as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. V801V) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 22)
Consequence
COL4A5
NM_033380.3 inframe_deletion
NM_033380.3 inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.47
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 Uncertain_significance. Variant got 5 ACMG points.
PM1
?
In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 2 uncertain in NM_033380.3
PM4
?
Nonframeshift variant in NON repetitive region in NM_033380.3.
PP5
?
Variant X-108614917-TTGGACCAAATGGACAACC-T is Pathogenic according to our data. Variant chrX-108614917-TTGGACCAAATGGACAACC-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.2411_2428del | p.Asn804_Pro809del | inframe_deletion | 30/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.2411_2428del | p.Asn804_Pro809del | inframe_deletion | 30/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000483338.1 | c.1235_1252del | p.Asn412_Pro417del | inframe_deletion | 14/20 | 1 | |||
COL4A5 | ENST00000361603.7 | c.2411_2428del | p.Asn804_Pro809del | inframe_deletion | 30/51 | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at