17-68555742-G-A
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1PM2PP3PP5_Very_Strong
The NM_017565.4(FAM20A):c.406C>T(p.Arg136Ter) variant causes a stop gained, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_017565.4 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM20A | NM_017565.4 | c.406C>T | p.Arg136Ter | stop_gained, splice_region_variant | 2/11 | ENST00000592554.2 | NP_060035.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM20A | ENST00000592554.2 | c.406C>T | p.Arg136Ter | stop_gained, splice_region_variant | 2/11 | 1 | NM_017565.4 | ENSP00000468308 | P1 | |
FAM20A | ENST00000226094.9 | n.63C>T | splice_region_variant, non_coding_transcript_exon_variant | 2/11 | 1 | |||||
FAM20A | ENST00000592847.1 | n.48C>T | splice_region_variant, non_coding_transcript_exon_variant | 2/8 | 3 | |||||
FAM20A | ENST00000590074.5 | c.*179C>T | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 3/12 | 2 | ENSP00000464910 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251298Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135852
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727164
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74410
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 27, 2022 | Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 28086997, 18597613, 28694781, 23468644, 21549343, 23434854) - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 11, 2023 | This premature translational stop signal has been observed in individual(s) with amelogenesis imperfecta and/or enamel-renal syndrome (PMID: 21549343, 23434854, 28086997). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 30879). This variant is present in population databases (rs144411158, gnomAD 0.04%). This sequence change creates a premature translational stop signal (p.Arg136*) in the FAM20A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FAM20A are known to be pathogenic (PMID: 21990045, 23434854). - |
Amelogenesis imperfecta type 1G Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 09, 2022 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at