6-47478236-G-GC
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000359314.5(CD2AP):c.-4dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000705 in 1,419,040 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )
Consequence
CD2AP
ENST00000359314.5 5_prime_UTR
ENST00000359314.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.160
Genes affected
CD2AP (HGNC:14258): (CD2 associated protein) This gene encodes a scaffolding molecule that regulates the actin cytoskeleton. The protein directly interacts with filamentous actin and a variety of cell membrane proteins through multiple actin binding sites, SH3 domains, and a proline-rich region containing binding sites for SH3 domains. The cytoplasmic protein localizes to membrane ruffles, lipid rafts, and the leading edges of cells. It is implicated in dynamic actin remodeling and membrane trafficking that occurs during receptor endocytosis and cytokinesis. Haploinsufficiency of this gene is implicated in susceptibility to glomerular disease. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CD2AP | NM_012120.3 | c.-4dup | 5_prime_UTR_variant | 1/18 | ENST00000359314.5 | NP_036252.1 | ||
| CD2AP | XM_005248976.2 | c.-4dup | 5_prime_UTR_variant | 1/18 | XP_005249033.1 | |||
| CD2AP | XM_017010641.2 | c.-4dup | 5_prime_UTR_variant | 1/14 | XP_016866130.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CD2AP | ENST00000359314.5 | c.-4dup | 5_prime_UTR_variant | 1/18 | 1 | NM_012120.3 | ENSP00000352264 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000572 AC: 1AN: 174698Hom.: 0 AF XY: 0.0000106 AC XY: 1AN XY: 94652
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GnomAD4 exome AF: 7.05e-7 AC: 1AN: 1419040Hom.: 0 Cov.: 35 AF XY: 0.00000142 AC XY: 1AN XY: 701858
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GnomAD4 genome
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Focal segmental glomerulosclerosis Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at