NM_001032221.6(STXBP1):c.1634T>G (p.Val545Gly) AND Developmental and epileptic encephalopathy, 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 25, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003324114.1

Allele description [Variation Report for NM_001032221.6(STXBP1):c.1634T>G (p.Val545Gly)]

NM_001032221.6(STXBP1):c.1634T>G (p.Val545Gly)

Gene:

STXBP1:syntaxin binding protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.1634T>G (p.Val545Gly)

HGVS:

NC_000009.12:g.127682492T>G
NG_016623.1:g.75286T>G
NG_016623.2:g.75582T>G
NM_001032221.6:c.1634T>GMANE SELECT
NM_001374306.2:c.1625T>G
NM_001374307.2:c.1592T>G
NM_001374308.2:c.1592T>G
NM_001374309.2:c.1592T>G
NM_001374310.2:c.1592T>G
NM_001374311.2:c.1592T>G
NM_001374312.2:c.1592T>G
NM_001374313.2:c.1634T>G
NM_001374314.1:c.1634T>G
NM_001374315.2:c.1526T>G
NM_003165.6:c.1634T>G
NP_001027392.1:p.Val545Gly
NP_001361235.1:p.Val542Gly
NP_001361236.1:p.Val531Gly
NP_001361237.1:p.Val531Gly
NP_001361238.1:p.Val531Gly
NP_001361239.1:p.Val531Gly
NP_001361240.1:p.Val531Gly
NP_001361241.1:p.Val531Gly
NP_001361242.1:p.Val545Gly
NP_001361243.1:p.Val545Gly
NP_001361244.1:p.Val509Gly
NP_003156.1:p.Val545Gly
NC_000009.11:g.130444771T>G

Protein change:

V509G

Molecular consequence:

NM_001032221.6:c.1634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374306.2:c.1625T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374307.2:c.1592T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374308.2:c.1592T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374309.2:c.1592T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374310.2:c.1592T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374311.2:c.1592T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374312.2:c.1592T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374313.2:c.1634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374314.1:c.1634T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374315.2:c.1526T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003165.6:c.1634T>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Developmental and epileptic encephalopathy, 4 (DEE4)
Synonyms:: Early infantile epileptic encephalopathy 4; STXBP1-Related Epileptic Encephalopathy
Identifiers:: MONDO: MONDO:0012812; MedGen: C2677326; Orphanet: 1934; Orphanet: 33069; OMIM: 612164

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004028540	Pediatrics Genetics, Post Graduate Institute of Medical Education and Research	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 25, 2023)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004028540

Pediatrics Genetics, Post Graduate Institute of Medical Education and Research

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 25, 2023)

de novo

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
North Indian	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Pediatrics Genetics, Post Graduate Institute of Medical Education and Research, SCV004028540.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	North Indian	1	not provided	not provided	clinical testing	PubMed (1)

Description

This is a novel variant, not reported in gnomAD population databases (PM2), PM1, PP2, PP3. This is an Exonic hotspot: 9 pathogenic or likely pathogenic reported variants were found in a 70bp region surrounding this variant in exon 18 within the region 127682490-127682560 without any missense benign variants.Gnomad constraint of missense upper Z-score for gene is greater than 3.09 Gene score: 4.263

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 3, 2023

ClinVar

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