rs760462252
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_ModeratePP5_Moderate
The NM_000091.5(COL4A3):c.4382C>T(p.Pro1461Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1461T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000091.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A3 | NM_000091.5 | c.4382C>T | p.Pro1461Leu | missense_variant | 48/52 | ENST00000396578.8 | |
MFF-DT | NR_102371.1 | n.48-2184G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A3 | ENST00000396578.8 | c.4382C>T | p.Pro1461Leu | missense_variant | 48/52 | 1 | NM_000091.5 | P1 | |
MFF-DT | ENST00000439598.6 | n.48-2184G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249496Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135350
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461840Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727220
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
Autosomal dominant Alport syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Fundacion Rioja Salud, Center for Biomedical Research (CIBIR) | Mar 18, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at