7-256001-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_020223.4(FAM20C):c.1225C>T(p.Arg409Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000065 in 1,383,674 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 Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R409H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_020223.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM20C | NM_020223.4 | c.1225C>T | p.Arg409Cys | missense_variant | Exon 6 of 10 | ENST00000313766.6 | NP_064608.2 | |
FAM20C | XR_001744837.2 | n.*66C>T | downstream_gene_variant | |||||
FAM20C | XR_007060116.1 | n.*66C>T | downstream_gene_variant | |||||
FAM20C | XR_007060117.1 | n.*52C>T | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM20C | ENST00000313766.6 | c.1225C>T | p.Arg409Cys | missense_variant | Exon 6 of 10 | 1 | NM_020223.4 | ENSP00000322323.5 | ||
FAM20C | ENST00000515795.1 | n.882C>T | non_coding_transcript_exon_variant | Exon 3 of 7 | 1 | |||||
FAM20C | ENST00000512382.1 | n.-194C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000714 AC: 1AN: 140084Hom.: 0 AF XY: 0.0000133 AC XY: 1AN XY: 75242
GnomAD4 exome AF: 0.00000650 AC: 9AN: 1383674Hom.: 0 Cov.: 32 AF XY: 0.00000586 AC XY: 4AN XY: 682792
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Neonatal death;C0424503:Abnormal facial shape;C0431380:Cortical dysplasia;CN228280:Severe brain malformation Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at