rs397515561
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_005982.4(SIX1):c.334C>T(p.Arg112Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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 not provided (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R112G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005982.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIX1 | NM_005982.4 | c.334C>T | p.Arg112Cys | missense_variant | 1/2 | ENST00000645694.3 | |
SIX1 | XM_017021602.3 | c.334C>T | p.Arg112Cys | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIX1 | ENST00000645694.3 | c.334C>T | p.Arg112Cys | missense_variant | 1/2 | NM_005982.4 | P1 | ||
SIX1 | ENST00000554986.2 | c.42-2279C>T | intron_variant | 3 | |||||
SIX1 | ENST00000553535.2 | n.249-2279C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
SIX1 | ENST00000555955.3 | n.1198-2279C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Branchiootic syndrome 3 Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at