rs1135401819
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP2PP3_ModeratePP5_Moderate
The NM_001032221.6(STXBP1):c.1706C>T(p.Ser569Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. S569S) has been classified as Benign.
Frequency
Consequence
NM_001032221.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STXBP1 | NM_001032221.6 | c.1706C>T | p.Ser569Phe | missense_variant | 19/19 | ENST00000373299.5 | |
STXBP1 | NM_003165.6 | c.*20C>T | 3_prime_UTR_variant | 20/20 | ENST00000373302.8 | ||
MIR3911 | NR_037473.1 | n.18G>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP1 | ENST00000373299.5 | c.1706C>T | p.Ser569Phe | missense_variant | 19/19 | 1 | NM_001032221.6 | A1 | |
STXBP1 | ENST00000373302.8 | c.*20C>T | 3_prime_UTR_variant | 20/20 | 1 | NM_003165.6 | P3 | ||
ENST00000624141.1 | n.63G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
MIR3911 | ENST00000577791.1 | n.18G>A | mature_miRNA_variant | 1/1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Non-syndromic intellectual disability Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris | Jan 06, 2017 | non syndromic mild Intellectual disability - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at