NM_001130438.3(SPTAN1):c.5545C>T (p.Arg1849Trp) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 18, 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:: RCV000464908.6

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.5545C>T (p.Arg1849Trp)]

NM_001130438.3(SPTAN1):c.5545C>T (p.Arg1849Trp)

Gene:

SPTAN1:spectrin alpha, non-erythrocytic 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001130438.3(SPTAN1):c.5545C>T (p.Arg1849Trp)

Other names:

p.R1849W:CGG>TGG

HGVS:

NC_000009.12:g.128618053C>T
NG_027748.1:g.70496C>T
NM_001130438.3:c.5545C>TMANE SELECT
NM_001195532.2:c.5470C>T
NM_001363759.2:c.5545C>T
NM_001363765.2:c.5485C>T
NM_003127.4:c.5530C>T
NP_001123910.1:p.Arg1849Trp
NP_001182461.1:p.Arg1824Trp
NP_001350688.1:p.Arg1849Trp
NP_001350694.1:p.Arg1829Trp
NP_003118.2:p.Arg1844Trp
NC_000009.11:g.131380332C>T
NM_001130438.2:c.5545C>T

Protein change:

R1824W

Links:

dbSNP: rs148402616

NCBI 1000 Genomes Browser:

rs148402616

Molecular consequence:

NM_001130438.3:c.5545C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195532.2:c.5470C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363759.2:c.5545C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363765.2:c.5485C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003127.4:c.5530C>T - missense variant - [Sequence Ontology: SO:0001583]

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

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Ficedula albicollis isolate OC2 contig00514, whole genome shotgun sequence
Ficedula albicollis isolate OC2 contig00514, whole genome shotgun sequence
gi|376372204|gb|AGTO01000172.1||gnl AGTO01|contig00514

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000553140	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 18, 2023)	germline	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

SCV000553140

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 18, 2023)

germline

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000553140.5

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

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1849 of the SPTAN1 protein (p.Arg1849Trp). This variant is present in population databases (rs148402616, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SPTAN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 207376). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SPTAN1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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