X-108440164-CTT-C
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_033380.3(COL4A5):c.40_41delTT(p.Leu14ThrfsTer25) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_033380.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.40_41delTT | p.Leu14ThrfsTer25 | frameshift_variant | Exon 1 of 53 | ENST00000328300.11 | NP_203699.1 | |
COL4A5 | NM_000495.5 | c.40_41delTT | p.Leu14ThrfsTer25 | frameshift_variant | Exon 1 of 51 | NP_000486.1 | ||
COL4A5 | XM_047441811.1 | c.40_41delTT | p.Leu14ThrfsTer25 | frameshift_variant | Exon 1 of 42 | XP_047297767.1 | ||
COL4A5 | XM_047441810.1 | c.-337_-336delTT | 5_prime_UTR_variant | Exon 1 of 54 | XP_047297766.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 20
GnomAD4 genome Cov.: 20
ClinVar
Submissions by phenotype
X-linked Alport syndrome Pathogenic:1
NM_000495.4(COL4A5):c.40_41delTT(L14Tfs*25) is expected to be pathogenic in the context of X-linked Alport syndrome. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in COL4A5, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.