NM_001130438.3(SPTAN1):c.5530G>C (p.Glu1844Gln) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 15, 2021
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:: RCV002922018.3

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.5530G>C (p.Glu1844Gln)]

NM_001130438.3(SPTAN1):c.5530G>C (p.Glu1844Gln)

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.5530G>C (p.Glu1844Gln)

HGVS:

NC_000009.12:g.128618038G>C
NG_027748.1:g.70481G>C
NG_027748.2:g.70453G>C
NM_001130438.3:c.5530G>CMANE SELECT
NM_001195532.2:c.5455G>C
NM_001363759.2:c.5530G>C
NM_001363765.2:c.5470G>C
NM_001375310.1:c.5530G>C
NM_001375311.2:c.5530G>C
NM_001375312.2:c.5566G>C
NM_001375313.1:c.5530G>C
NM_001375314.2:c.5470G>C
NM_001375318.1:c.5566G>C
NM_003127.4:c.5515G>C
NP_001123910.1:p.Glu1844Gln
NP_001182461.1:p.Glu1819Gln
NP_001350688.1:p.Glu1844Gln
NP_001350694.1:p.Glu1824Gln
NP_001362239.1:p.Glu1844Gln
NP_001362240.1:p.Glu1844Gln
NP_001362241.2:p.Glu1856Gln
NP_001362242.1:p.Glu1844Gln
NP_001362243.1:p.Glu1824Gln
NP_001362247.1:p.Glu1856Gln
NP_003118.2:p.Glu1839Gln
NC_000009.11:g.131380317G>C

Protein change:

E1819Q

Molecular consequence:

NM_001130438.3:c.5530G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195532.2:c.5455G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363759.2:c.5530G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001363765.2:c.5470G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375310.1:c.5530G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375311.2:c.5530G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375312.2:c.5566G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375313.1:c.5530G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375314.2:c.5470G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375318.1:c.5566G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003127.4:c.5515G>C - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003258883	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 15, 2021)	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

SCV003258883

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 15, 2021)

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, SCV003258883.2

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

Description

This variant has not been reported in the literature in individuals affected with SPTAN1-related conditions. This variant is present in population databases (rs763507558, gnomAD 0.003%). This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 1844 of the SPTAN1 protein (p.Glu1844Gln). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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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