NM_001032221.6(STXBP1):c.754_755del (p.Met252fs) AND Early infantile epileptic encephalopathy with suppression bursts

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 12, 2022
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:: RCV001850006.4

Allele description

NM_001032221.6(STXBP1):c.754_755del (p.Met252fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.754_755del (p.Met252fs)

HGVS:

NC_000009.12:g.127666256_127666257del
NG_016623.1:g.59050_59051del
NM_001032221.6:c.754_755delMANE SELECT
NM_001374306.2:c.745_746del
NM_001374307.2:c.712_713del
NM_001374308.2:c.712_713del
NM_001374309.2:c.712_713del
NM_001374310.2:c.712_713del
NM_001374311.2:c.712_713del
NM_001374312.2:c.712_713del
NM_001374313.2:c.754_755del
NM_001374314.1:c.754_755del
NM_001374315.2:c.754_755del
NM_003165.6:c.754_755del
NP_001027392.1:p.Met252fs
NP_001361235.1:p.Met249fs
NP_001361236.1:p.Met238fs
NP_001361237.1:p.Met238fs
NP_001361238.1:p.Met238fs
NP_001361239.1:p.Met238fs
NP_001361240.1:p.Met238fs
NP_001361241.1:p.Met238fs
NP_001361242.1:p.Met252fs
NP_001361243.1:p.Met252fs
NP_001361244.1:p.Met252fs
NP_003156.1:p.Met252fs
NC_000009.11:g.130428534_130428535del
NC_000009.11:g.130428535_130428536del
NM_001032221.3:c.754_755del

Protein change:

M238fs

Links:

dbSNP: rs587784454

NCBI 1000 Genomes Browser:

rs587784454

Molecular consequence:

NM_001032221.6:c.754_755del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374306.2:c.745_746del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374307.2:c.712_713del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374308.2:c.712_713del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374309.2:c.712_713del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374310.2:c.712_713del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374311.2:c.712_713del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374312.2:c.712_713del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374313.2:c.754_755del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374314.1:c.754_755del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001374315.2:c.754_755del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003165.6:c.754_755del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Early infantile epileptic encephalopathy with suppression bursts (EIEE)
Synonyms:: Early infantile epileptic encephalopathy; Ohtahara syndrome; Developmental and epileptic encephalopathy
Identifiers:: MONDO: MONDO:0100062; MedGen: C0393706; Orphanet: 1934; OMIM: PS308350

Recent activity

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putative manganese-dependent inorganic diphosphatase [Geothermobacter hydrogenip...
putative manganese-dependent inorganic diphosphatase [Geothermobacter hydrogeniphilus]
gi|1334970650|ref|WP_103114773.1|

Protein
nssv1635017 (2)
dbVar
Bos taurus ubiquitin cross-reactive protein (UCRP) mRNA, complete cds
Bos taurus ubiquitin cross-reactive protein (UCRP) mRNA, complete cds
gi|2098775|gb|U96014.1|BTU96014

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002243375	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 12, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25693842, 20887364, 26384463, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002243375

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 12, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Characterization of patients referred for non-specific intellectual disability testing: the importance of autosomal genes for diagnosis.

Tan CA, Topper S, Del Gaudio D, Nelakuditi V, Shchelochkov O, Nowaczyk MJM, Zeesman S, Brady L, Russell L, Meeks N, Sastry S, Arndt K, Kobiernicki F, Shaw R, Das S.

Clin Genet. 2016 Apr;89(4):478-483. doi: 10.1111/cge.12575. Epub 2015 Mar 15.

PubMed [citation]

PMID:: 25693842

STXBP1 mutations in early infantile epileptic encephalopathy with suppression-burst pattern.

Saitsu H, Kato M, Okada I, Orii KE, Higuchi T, Hoshino H, Kubota M, Arai H, Tagawa T, Kimura S, Sudo A, Miyama S, Takami Y, Watanabe T, Nishimura A, Nishiyama K, Miyake N, Wada T, Osaka H, Kondo N, Hayasaka K, Matsumoto N.

Epilepsia. 2010 Dec;51(12):2397-405. doi: 10.1111/j.1528-1167.2010.02728.x. Epub 2010 Sep 30.

PubMed [citation]

PMID:: 20887364

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002243375.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 160071). This premature translational stop signal has been observed in individual(s) with STXBP1-related conditions (PMID: 25693842). 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 creates a premature translational stop signal (p.Met252Glufs*3) in the STXBP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in STXBP1 are known to be pathogenic (PMID: 20887364, 26384463).

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

Last Updated: Feb 14, 2024

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