NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3]) AND Early infantile epileptic encephalopathy with suppression bursts

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 13, 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:: RCV000696609.17

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3])]

NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3])

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001130438.3(SPTAN1):c.6899ACCAGCTGG[3] (p.2300DQL[3])

HGVS:

NC_000009.12:g.128632263ACCAGCTGG[3]
NG_027748.1:g.84706ACCAGCTGG[3]
NG_034056.1:g.29573AGCTGGTCC[3]
NM_001130438.2:c.6908_6916dup9
NM_001130438.3:c.6899ACCAGCTGG[3]MANE SELECT
NM_001195532.2:c.6824ACCAGCTGG[3]
NM_001363759.2:c.6962ACCAGCTGG[3]
NM_001363765.2:c.6839ACCAGCTGG[3]
NM_001375310.1:c.6986ACCAGCTGG[3]
NM_001375311.2:c.6899ACCAGCTGG[3]
NM_001375312.2:c.6935ACCAGCTGG[3]
NM_001375313.1:c.6881ACCAGCTGG[3]
NM_001375314.2:c.6839ACCAGCTGG[3]
NM_001375318.1:c.6998ACCAGCTGG[3]
NM_003127.4:c.6884ACCAGCTGG[3]
NP_001123910.1:p.2300DQL[3]
NP_001182461.1:p.2275DQL[3]
NP_001350688.1:p.2321DQL[3]
NP_001350694.1:p.2280DQL[3]
NP_001362239.1:p.2329DQL[3]
NP_001362240.1:p.2300DQL[3]
NP_001362241.2:p.2312DQL[3]
NP_001362242.1:p.2294DQL[3]
NP_001362243.1:p.2280DQL[3]
NP_001362247.1:p.2333DQL[3]
NP_003118.2:p.2295DQL[3]
NC_000009.11:g.131394539_131394540insGGACCAGCT
NC_000009.11:g.131394542ACCAGCTGG[3]
NC_000009.12:g.128632260_128632261insGGACCAGCT
NM_001130438.2:c.6908_6916dupACCAGCTGG
NM_001130438.3:c.6908_6916dupMANE SELECT
NM_003127.4:c.6881_6882insGGACCAGCT
p.D2303_L2305dup
p.Leu2305_Gly2306insAspGlnLeu

Links:

OMIM: 182810.0005; dbSNP: rs587784440

NCBI 1000 Genomes Browser:

rs587784440

Molecular consequence:

NM_001130438.3:c.6899ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001195532.2:c.6824ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001363759.2:c.6962ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001363765.2:c.6839ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375310.1:c.6986ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375311.2:c.6899ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375312.2:c.6935ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375313.1:c.6881ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375314.2:c.6839ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001375318.1:c.6998ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_003127.4:c.6884ACCAGCTGG[3] - inframe_insertion - [Sequence Ontology: SO:0001821]

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

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000825175	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 13, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22656320, 29050398, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000825175

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 13, 2022)

germline

clinical testing

PubMed (3)
[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

Progressive diffuse brain atrophy in West syndrome with marked hypomyelination due to SPTAN1 gene mutation.

Nonoda Y, Saito Y, Nagai S, Sasaki M, Iwasaki T, Matsumoto N, Ishii M, Saitsu H.

Brain Dev. 2013 Mar;35(3):280-3. doi: 10.1016/j.braindev.2012.05.002. Epub 2012 May 31.

PubMed [citation]

PMID:: 22656320

Delineating SPTAN1 associated phenotypes: from isolated epilepsy to encephalopathy with progressive brain atrophy.

Syrbe S, Harms FL, Parrini E, Montomoli M, Mütze U, Helbig KL, Polster T, Albrecht B, Bernbeck U, van Binsbergen E, Biskup S, Burglen L, Denecke J, Heron B, Heyne HO, Hoffmann GF, Hornemann F, Matsushige T, Matsuura R, Kato M, Korenke GC, Kuechler A, et al.

Brain. 2017 Sep 1;140(9):2322-2336. doi: 10.1093/brain/awx195.

PubMed [citation]

PMID:: 29050398
PMCID:: PMC6248409

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000825175.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

ClinVar contains an entry for this variant (Variation ID: 160028). This variant has been observed in individual(s) with West syndrome (PMID: 22656320, 29050398). 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 variant, c.6908_6916dup, results in the insertion of 3 amino acid(s) of the SPTAN1 protein (p.Asp2303_Leu2305dup), but otherwise preserves the integrity of the reading frame. Experimental studies have shown that this variant affects SPTAN1 function (PMID: 29050398). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant.

#	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: Oct 8, 2024

ClinVar

Relating variation to medicine