NM_001130438.3(SPTAN1):c.6184C>T (p.Arg2062Trp) AND Developmental and epileptic encephalopathy, 5

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jul 15, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001780272.4

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.6184C>T (p.Arg2062Trp)]

NM_001130438.3(SPTAN1):c.6184C>T (p.Arg2062Trp)

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.6184C>T (p.Arg2062Trp)

HGVS:

NC_000009.12:g.128625883C>T
NG_027748.1:g.78326C>T
NM_001130438.3:c.6184C>TMANE SELECT
NM_001195532.2:c.6109C>T
NM_001363759.2:c.6184C>T
NM_001363765.2:c.6124C>T
NM_001375310.1:c.6184C>T
NM_001375311.2:c.6184C>T
NM_001375312.2:c.6220C>T
NM_001375313.1:c.6184C>T
NM_001375314.2:c.6124C>T
NM_001375318.1:c.6220C>T
NM_003127.4:c.6169C>T
NP_001123910.1:p.Arg2062Trp
NP_001182461.1:p.Arg2037Trp
NP_001350688.1:p.Arg2062Trp
NP_001350694.1:p.Arg2042Trp
NP_001362239.1:p.Arg2062Trp
NP_001362240.1:p.Arg2062Trp
NP_001362241.2:p.Arg2074Trp
NP_001362242.1:p.Arg2062Trp
NP_001362243.1:p.Arg2042Trp
NP_001362247.1:p.Arg2074Trp
NP_003118.2:p.Arg2057Trp
NC_000009.11:g.131388162C>T
NM_001130438.2:c.6184C>T

Protein change:

R2037W

Links:

dbSNP: rs2131953982

NCBI 1000 Genomes Browser:

rs2131953982

Molecular consequence:

NM_001130438.3:c.6184C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195532.2:c.6109C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363759.2:c.6184C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363765.2:c.6124C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375310.1:c.6184C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375311.2:c.6184C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375312.2:c.6220C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375313.1:c.6184C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375314.2:c.6124C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001375318.1:c.6220C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003127.4:c.6169C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 5 (DEE5)
Synonyms:: Early infantile epileptic encephalopathy 5
Identifiers:: MONDO: MONDO:0013277; MedGen: C3150731; Orphanet: 3451; OMIM: 613477

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002026323	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 1, 2017)	de novo	research	PubMed (2) [See all records that cite these PMIDs] 29050398, 25741868
SCV002056577	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 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

SCV002026323

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 1, 2017)

de novo

research

PubMed (2)
[See all records that cite these PMIDs]

SCV002056577

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jul 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	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	de novo	unknown	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

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

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 Institute of Human Genetics, University of Leipzig Medical Center, SCV002026323.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (2)

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

From Genome-Nilou Lab, SCV002056577.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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