rs387907321
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_001080414.4(CCDC88C):c.5841_5842delAG(p.Glu1949GlyfsTer26) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000657 in 152,236 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_001080414.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC88C | ENST00000389857.11 | c.5841_5842delAG | p.Glu1949GlyfsTer26 | frameshift_variant | Exon 30 of 30 | 5 | NM_001080414.4 | ENSP00000374507.6 | ||
CCDC88C | ENST00000556726 | c.*1675_*1676delAG | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000452406.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
Hydrocephalus, nonsyndromic, autosomal recessive 1 Pathogenic:1
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Congenital hydrocephalus Pathogenic:1
The homozygous p.Glu1949GlyfsTer26 variant in CCDC88C was identified by our study in one individual with congenital hydrocephalus, global developmental delay, and seizures. The p.Glu1949GlyfsTer26 variant in CCDC88C has been previously reported in five affected siblings from one family with congenital hydrocephalus 1 (PMID: 23042809), but has been identified in 0.008% (1/125568) chromosomes by TopMed (https://bravo.sph.umich.edu/, dbSNP ID: rs387907321). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. These affected individuals (PMID: 23042809) and the individual identified by our study were homozygotes, which increases the likelihood that the p.Glu1949GlyfsTer26 variant is pathogenic. This variant has also been reported in ClinVar (Variation ID: 39862) and has been interpreted as pathogenic by OMIM. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1393 and leads to a premature termination codon 19 amino acids downstream. This termination codon occurs within the terminal 50 bases of the last exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. Loss of function of the CCDC88C gene is strongly associated to autosomal recessive congenital hydrocephalus 1. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive congenital hydrocephalus 1. ACMG/AMP Criteria applied: PVS1_Supporting, PM2_Supporting, PM3, PP1_Strong (Richards 2015). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at