chr5-44305045-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_004465.2(FGF10):c.577C>T(p.Arg193*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,672 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 (★★).
Frequency
Consequence
NM_004465.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FGF10 | NM_004465.2 | c.577C>T | p.Arg193* | stop_gained | Exon 3 of 3 | ENST00000264664.5 | NP_004456.1 | |
FGF10 | XM_005248264.5 | c.577C>T | p.Arg193* | stop_gained | Exon 4 of 4 | XP_005248321.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461672Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727138
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Congenital absence of salivary gland Pathogenic:2
The variant is not observed in the gnomAD v2.1.1 dataset. The variant is predicted to result in a loss or disruption of normal protein function through protein truncation. The predicted truncated protein may be shortened by less than 10%. The variant has been reported to co-segregate with the disease in at least 3 similarly affected relatives/individuals in the same family or similarly affected unrelated families (PMID: 15654336). The variant has been reported to be associated with FGF10 -related disorder (ClinVar ID: VCV000007529 / PMID: 15654336). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline. -
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not provided Pathogenic:1
The R193X variant in the FGF10 gene has been reported previously in association with ALSG in multiple affected members of a Swedish family (Entesarian et al., 2005). Additionally, two of the individuals from that same family were included in a group of individuals with loss of function variants in FGF10 who were found to have decreased lung function parameters compared to controls (Klar et al., 2011). This variant is predicted to cause loss of normal protein function through protein truncation as the last 16 amino acids of the protein are lost. The R193X variant is not observed in large population cohorts (Lek et al., 2016). We interpret R193X as a pathogenic variant. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at