rs200786329
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM1PP2BP4BP6BS2
The NM_001845.6(COL4A1):c.1055C>T(p.Pro352Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000409 in 1,614,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P352Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001845.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL4A1 | ENST00000375820.10 | c.1055C>T | p.Pro352Leu | missense_variant | Exon 19 of 52 | 1 | NM_001845.6 | ENSP00000364979.4 | ||
COL4A1 | ENST00000543140.6 | c.1055C>T | p.Pro352Leu | missense_variant | Exon 19 of 25 | 1 | ENSP00000443348.1 | |||
COL4A1 | ENST00000647797.1 | c.932C>T | p.Pro311Leu | missense_variant | Exon 18 of 20 | ENSP00000497756.2 | ||||
COL4A1 | ENST00000649738.1 | n.1185C>T | non_coding_transcript_exon_variant | Exon 19 of 31 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251474Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135906
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727248
GnomAD4 genome AF: 0.000171 AC: 26AN: 152214Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74428
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
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Identified in patients with small vessel disease and intracranial hemorrhage in published literature (PMID: 22522439, 31719132, 35711275, Aref2024[article]); Functional studies suggest that p.(P352L) results in reduced ratio of extracelluar to intracellular COL4A1 compared to controls (PMID: 22522439); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29114093, 31857254, 34382650, Kiss2019, 22914737, 30518145, 22522439, 34426522, Aref2024[article], 31719132, 35711275, 30476936) -
Brain small vessel disease 1 with or without ocular anomalies Uncertain:1
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Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome Benign:1
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Hemorrhage, intracerebral, susceptibility to Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at