NM_003165.6:c.963G>C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong
The NM_003165.6(STXBP1):c.963G>C(p.Lys321Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. K321K) has been classified as Uncertain significance.
Frequency
Consequence
NM_003165.6 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STXBP1 | NM_003165.6 | c.963G>C | p.Lys321Asn | missense_variant, splice_region_variant | Exon 11 of 20 | ENST00000373302.8 | NP_003156.1 | |
STXBP1 | NM_001032221.6 | c.963G>C | p.Lys321Asn | missense_variant, splice_region_variant | Exon 11 of 19 | ENST00000373299.5 | NP_001027392.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373302.8 | c.963G>C | p.Lys321Asn | missense_variant, splice_region_variant | Exon 11 of 20 | 1 | NM_003165.6 | ENSP00000362399.3 | ||
STXBP1 | ENST00000373299.5 | c.963G>C | p.Lys321Asn | missense_variant, splice_region_variant | Exon 11 of 19 | 1 | NM_001032221.6 | ENSP00000362396.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at