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NM_001130438.3(SPTAN1):c.4640T>A (p.Leu1547Gln) AND Developmental and epileptic encephalopathy, 5

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 14, 2021
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001328004.3

Allele description

NM_001130438.3(SPTAN1):c.4640T>A (p.Leu1547Gln)

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.4640T>A (p.Leu1547Gln)
HGVS:
  • NC_000009.12:g.128609166T>A
  • NG_027748.1:g.61609T>A
  • NM_001130438.3:c.4640T>AMANE SELECT
  • NM_001195532.2:c.4580T>A
  • NM_001363759.2:c.4640T>A
  • NM_001363765.2:c.4580T>A
  • NM_001375310.1:c.4640T>A
  • NM_001375311.2:c.4640T>A
  • NM_001375312.2:c.4676T>A
  • NM_001375313.1:c.4640T>A
  • NM_001375314.2:c.4580T>A
  • NM_001375318.1:c.4676T>A
  • NM_003127.4:c.4640T>A
  • NP_001123910.1:p.Leu1547Gln
  • NP_001182461.1:p.Leu1527Gln
  • NP_001350688.1:p.Leu1547Gln
  • NP_001350694.1:p.Leu1527Gln
  • NP_001362239.1:p.Leu1547Gln
  • NP_001362240.1:p.Leu1547Gln
  • NP_001362241.2:p.Leu1559Gln
  • NP_001362242.1:p.Leu1547Gln
  • NP_001362243.1:p.Leu1527Gln
  • NP_001362247.1:p.Leu1559Gln
  • NP_003118.2:p.Leu1547Gln
  • NC_000009.11:g.131371445T>A
Protein change:
L1527Q
Links:
dbSNP: rs1856289676
NCBI 1000 Genomes Browser:
rs1856289676
Molecular consequence:
  • NM_001130438.3:c.4640T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195532.2:c.4580T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363759.2:c.4640T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363765.2:c.4580T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375310.1:c.4640T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375311.2:c.4640T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375312.2:c.4676T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375313.1:c.4640T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375314.2:c.4580T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375318.1:c.4676T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003127.4:c.4640T>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
protein truncation [Variation Ontology: 0015]
Observations:
1

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001519335HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP)
no assertion criteria provided
Likely pathogenic
(Jan 14, 2021) 		de novoclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Caucasiande novoyes1not providednot providednot providednot providedclinical testing

Details of each submission

From HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP), SCV001519335.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testingnot provided

Description

The variant was detected in a 4-year-old boy with generalized tonic-clonic epilepsy. The c.4640T>A variant in the SPTAN1 gene (NM_001130438.3) consists of an amino acid change (p.Leu1547Gln). This alteration has not been reported previously in the literature and it is not detected in the general population. The in-silico tools predict that it is very likely to affect the protein function. Pathological variants in the SPTAN1 gene are associated with the phenotype of Developmental and epileptic encephalopathy 5 (OMIM: 613477) with autosomal dominant inheritance. The genetic study of the parents was carried out using the Sanger sequencing method and they did not present the alteration, so it is a de novo variant in the child. Therefore, the clinical significance of the c.4640T>A variant is likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024