rs118203945
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The ENST00000376810.6(UBIAD1):āc.305A>Gā(p.Asn102Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
ENST00000376810.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UBIAD1 | NM_013319.3 | c.305A>G | p.Asn102Ser | missense_variant | 1/2 | ENST00000376810.6 | NP_037451.1 | |
UBIAD1 | NM_001330349.2 | c.305A>G | p.Asn102Ser | missense_variant | 1/3 | NP_001317278.1 | ||
UBIAD1 | NM_001330350.2 | c.305A>G | p.Asn102Ser | missense_variant | 1/2 | NP_001317279.1 | ||
UBIAD1 | XM_047418727.1 | c.305A>G | p.Asn102Ser | missense_variant | 1/3 | XP_047274683.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UBIAD1 | ENST00000376810.6 | c.305A>G | p.Asn102Ser | missense_variant | 1/2 | 1 | NM_013319.3 | ENSP00000366006 | P1 | |
UBIAD1 | ENST00000376804.2 | c.305A>G | p.Asn102Ser | missense_variant | 1/2 | 2 | ENSP00000366000 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Schnyder crystalline corneal dystrophy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at