NM_001130438.3(SPTAN1):c.5017A>G (p.Lys1673Glu) AND Developmental and epileptic encephalopathy, 5

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 1, 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:: RCV002226864.2

Allele description [Variation Report for NM_001130438.3(SPTAN1):c.5017A>G (p.Lys1673Glu)]

NM_001130438.3(SPTAN1):c.5017A>G (p.Lys1673Glu)

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.5017A>G (p.Lys1673Glu)

HGVS:

NC_000009.12:g.128612220A>G
NG_027748.1:g.64663A>G
NM_001130438.3:c.5017A>GMANE SELECT
NM_001195532.2:c.4942A>G
NM_001363759.2:c.5017A>G
NM_001363765.2:c.4957A>G
NM_001375310.1:c.5017A>G
NM_001375311.2:c.5017A>G
NM_001375312.2:c.5053A>G
NM_001375313.1:c.5017A>G
NM_001375314.2:c.4957A>G
NM_001375318.1:c.5053A>G
NM_003127.4:c.5002A>G
NP_001123910.1:p.Lys1673Glu
NP_001182461.1:p.Lys1648Glu
NP_001350688.1:p.Lys1673Glu
NP_001350694.1:p.Lys1653Glu
NP_001362239.1:p.Lys1673Glu
NP_001362240.1:p.Lys1673Glu
NP_001362241.2:p.Lys1685Glu
NP_001362242.1:p.Lys1673Glu
NP_001362243.1:p.Lys1653Glu
NP_001362247.1:p.Lys1685Glu
NP_003118.2:p.Lys1668Glu
NC_000009.11:g.131374499A>G
NM_001130438.2:c.5017A>G

Protein change:

K1648E

Links:

dbSNP: rs2131682815

NCBI 1000 Genomes Browser:

rs2131682815

Molecular consequence:

NM_001130438.3:c.5017A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001195532.2:c.4942A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001363759.2:c.5017A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001363765.2:c.4957A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375310.1:c.5017A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375311.2:c.5017A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375312.2:c.5053A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375313.1:c.5017A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375314.2:c.4957A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375318.1:c.5053A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003127.4:c.5002A>G - 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
SCV002505754	Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 1, 2021)	de novo	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

SCV002505754

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 1, 2021)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, SCV002505754.2

#	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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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