rs121918317

Positions:

• chr9-127682489-G-A
• chr9-127682489-G-T

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The ENST00000373299.5(STXBP1):​c.1631G>A​(p.Gly544Asp) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G544C) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: STXBP1 ENST00000373299.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 9.86

Genes affected

STXBP1 (HGNC:11444): (syntaxin binding protein 1) This gene encodes a syntaxin-binding protein. The encoded protein appears to play a role in release of neurotransmitters via regulation of syntaxin, a transmembrane attachment protein receptor. Mutations in this gene have been associated with infantile epileptic encephalopathy-4. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Pathogenic. Variant got 19 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 6 uncertain in ENST00000373299.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr9-127682488-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 982594.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), STXBP1. . Gene score misZ 4.263 (greater than the threshold 3.09). Trascript score misZ 5.8379 (greater than threshold 3.09). GenCC has associacion of gene with intellectual disability, autosomal dominant non-syndromic intellectual disability, Dravet syndrome, undetermined early-onset epileptic encephalopathy, autism spectrum disorder, developmental and epileptic encephalopathy, West syndrome, atypical Rett syndrome, developmental and epileptic encephalopathy, 4.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant 9-127682489-G-A is Pathogenic according to our data. Variant chr9-127682489-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 6726.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-127682489-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STXBP1	NM_003165.6	c.1631G>A	p.Gly544Asp	missense_variant	18/20	ENST00000373302.8	NP_003156.1
STXBP1	NM_001032221.6	c.1631G>A	p.Gly544Asp	missense_variant	18/19	ENST00000373299.5	NP_001027392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STXBP1	ENST00000373302.8	c.1631G>A	p.Gly544Asp	missense_variant	18/20	1	NM_003165.6	ENSP00000362399	P3
STXBP1	ENST00000373299.5	c.1631G>A	p.Gly544Asp	missense_variant	18/19	1	NM_001032221.6	ENSP00000362396	A1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Developmental and epileptic encephalopathy, 4 Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 2008	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 26, 2023	Variant summary: STXBP1 c.1631G>A (p.Gly544Asp) results in a non-conservative amino acid change in the encoded protein sequence, altering a highly conserved residue (HGMD) predicted to be important for protein conformation (Saitsu_2008). Three other missense variants affecting this amino acid have been classified as pathogenic/likely pathogenic in ClinVar (p.G544R, p.G544C, p.G544V), suggesting this is a functionally important residue. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251440 control chromosomes. c.1631G>A has been reported in the literature in individuals affected with Developmental And Epileptic Encephalopathy (Saitsu_2008, Epi4K_2013, Geisheker_2017, Yuskaitis_2018), including de novo occurrences. These data indicate that the variant is likely to be associated with disease. One publication reported expression analysis of recombinant EGFP-STXBP1 proteins in N2A cells, finding clusters of protein aggregation in a subset of cells with the variant, suggesting possible protein instability (Saitsu_2008). No submitters have provided clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic. -

Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

May 20, 2023

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Gly544 amino acid residue in STXBP1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 23409955, 26514728). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects STXBP1 function (PMID: 18469812, 29538625). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt STXBP1 protein function. ClinVar contains an entry for this variant (Variation ID: 6726). This missense change has been observed in individual(s) with clinical features of early infantile epileptic encephalopathies (PMID: 18469812, 30174244). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 544 of the STXBP1 protein (p.Gly544Asp). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.46	.;T;.;T;.;T;D;D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D;.;D;D;D;D;D;D
M_CAP	Pathogenic	0.89	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.2	.;.;M;.;.;.;M;.
MutationTaster	Benign	1.0	A;A
PrimateAI	Pathogenic	0.86	D
PROVEAN	Pathogenic	-6.8	.;.;D;.;.;.;D;.
REVEL	Pathogenic	0.99
Sift	Uncertain	0.0010	.;.;D;.;.;.;D;.
Sift4G	Pathogenic	0.0	.;.;D;.;.;.;D;D
Polyphen		1.0	.;.;D;.;.;.;D;.
Vest4		1.0
MutPred		0.94		.;.;Loss of catalytic residue at V545 (P = 0.0873);Loss of catalytic residue at V545 (P = 0.0873);Loss of catalytic residue at V545 (P = 0.0873);.;Loss of catalytic residue at V545 (P = 0.0873);.;
MVP		0.96
MPC		2.8
ClinPred		1.0	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.97
gMVP		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121918317; hg19: chr9-130444768;