rs565866662
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 8P and 4B. PVS1BS2
The NM_183374.3(CYP26C1):c.845_851dupCCATGCA(p.Gln284HisfsTer129) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00248 in 1,613,456 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_183374.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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CYP26C1 | ENST00000651965.1 | c.845_851dupCCATGCA | p.Gln284HisfsTer129 | frameshift_variant | Exon 4 of 6 | NM_183374.3 | ENSP00000498424.1 | |||
ENSG00000285846 | ENST00000648258.1 | n.875_881dupCCATGCA | non_coding_transcript_exon_variant | Exon 1 of 4 | ||||||
CYP26C1 | ENST00000624358.3 | n.*1117-63_*1117-57dupCCATGCA | intron_variant | Intron 3 of 5 | 2 | ENSP00000485098.1 |
Frequencies
GnomAD3 genomes AF: 0.00204 AC: 311AN: 152214Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00211 AC: 529AN: 250796Hom.: 1 AF XY: 0.00218 AC XY: 295AN XY: 135520
GnomAD4 exome AF: 0.00252 AC: 3688AN: 1461124Hom.: 7 Cov.: 30 AF XY: 0.00237 AC XY: 1719AN XY: 726788
GnomAD4 genome AF: 0.00204 AC: 311AN: 152332Hom.: 1 Cov.: 33 AF XY: 0.00236 AC XY: 176AN XY: 74484
ClinVar
Submissions by phenotype
Focal facial dermal dysplasia type IV Pathogenic:2Uncertain:1
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PVS1, PS3, PS4, BS1 -
not provided Pathogenic:2Benign:1
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Published functional studies demonstrate a damaging effect with this variant demonstrating 4% of enzyme activity as compared to wild-type (PMID: 23161670); Frameshift variant predicted to result in abnormal protein length as the last 239 amino acid(s) are replaced with 128 different amino acid(s); This variant is associated with the following publications: (PMID: 32040484, 34426522, 23161670, 29263414) -
CYP26C1: PVS1, PM2, PM3, PP4 -
CYP26C1-related disorder Pathogenic:1
The CYP26C1 c.845_851dup7 variant is predicted to result in a frameshift and premature protein termination (p.Gln284Hisfs*129). This variant was reported in the compound heterozygous or homozygous state in multiple individuals with focal facial dermal dysplasia IV (Slavotinek et al. 2013. PubMed ID: 23161670, described as c.844_851dupCCATGCA; Lee et al. 2018. PubMed ID: 29263414). This variant is reported in 0.70% of alleles in individuals of European (Finnish) descent in gnomAD. This variant has also been observed in the heterozygous state in an individual with optic nerve hypoplasia (Table 2, Dahl et al. 2020. PubMed ID: 32040484). Frameshift variants in CYP26C1 are expected to be pathogenic. This variant is interpreted as pathogenic. -
not specified Uncertain:1
Variant classified as Uncertain Significance - Favor Pathogenic. The p.Gln284His fsX129 variant in CYP26C1 has been reported in 3 homozygous and 2 compound heter ozygous individuals with focal facial dermal dysplasia 4 (FFDD 4)and segregated with disease in 1 affected relative (Slavotinek 2013, Lee 2018). This variant is predicted to cause a frameshift, which alters the protein?s amino acid sequence beginning at position 284 and leads to a premature termination codon 129 amino acids downstream. This termination codon occurs within the terminal 50 bases of the second to last exon and is, therefore, likely to escape nonsense mediated de cay (NMD) and result in a truncated protein. This variant has also been identifi ed in 0.7% (177/25112) of Finnish and 0.3% (392/128808) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org), which is higher than expected cons idering the rarity of FFDD 4. It has been speculated that this is due to incompl ete penetrance or under ascertainment (Slavotinek 2013); however, it is unclear at this time. In summary, while there is some suspicion for a pathogenic role, t he clinical significance of the p.Gln284HisfsX129 variant is uncertain due to co nflicting data. ACMG/AMP Criteria applied: PM3, PM4, BS1_Supporting. -
Optic nerve hypoplasia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at