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NM_001199107.2(TBC1D24):c.686T>C (p.Phe229Ser) AND Developmental and epileptic encephalopathy, 16

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jan 27, 2023
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:
RCV000050233.17

Allele description [Variation Report for NM_001199107.2(TBC1D24):c.686T>C (p.Phe229Ser)]

NM_001199107.2(TBC1D24):c.686T>C (p.Phe229Ser)

Gene:
TBC1D24:TBC1 domain family member 24 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001199107.2(TBC1D24):c.686T>C (p.Phe229Ser)
HGVS:
  • NC_000016.10:g.2496834T>C
  • NG_028170.1:g.26689T>C
  • NM_001199107.2:c.686T>CMANE SELECT
  • NM_020705.3:c.686T>C
  • NP_001186036.1:p.Phe229Ser
  • NP_065756.1:p.Phe229Ser
  • NC_000016.9:g.2546835T>C
  • NM_001199107.1:c.686T>C
  • Q9ULP9:p.Phe229Ser
Protein change:
F229S; PHE229SER
Links:
UniProtKB: Q9ULP9#VAR_070102; OMIM: 613577.0005; dbSNP: rs397514713
NCBI 1000 Genomes Browser:
rs397514713
Molecular consequence:
  • NM_001199107.2:c.686T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020705.3:c.686T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Developmental and epileptic encephalopathy, 16 (DEE16)
Synonyms:
Early infantile epileptic encephalopathy 16
Identifiers:
MONDO: MONDO:0014133; MedGen: C3809173; Orphanet: 293181; Orphanet: 352596; OMIM: 615338

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000082812OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2013)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000211977Division of Medical Genetics; Sainte-Justine Hospital
no assertion criteria provided
Pathogenic
(Dec 22, 2014)
germlineliterature only

Citation Link,

SCV004045864Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Pathogenic
(Jan 27, 2023)
paternalclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedliterature only
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedpaternalyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Novel compound heterozygous mutations in TBC1D24 cause familial malignant migrating partial seizures of infancy.

Milh M, Falace A, Villeneuve N, Vanni N, Cacciagli P, Assereto S, Nabbout R, Benfenati F, Zara F, Chabrol B, Villard L, Fassio A.

Hum Mutat. 2013 Jun;34(6):869-72. doi: 10.1002/humu.22318. Epub 2013 Apr 12.

PubMed [citation]
PMID:
23526554

Details of each submission

From OMIM, SCV000082812.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In 2 sisters with developmental and epileptic encephalopathy-16 (DEE16; 615338), Milh et al. (2013) identified compound heterozygosity for 2 mutations in exon 2 of the TBC1D24 gene: a c.686T-C transition, resulting in a phe229-to-ser (F229S) substitution at a highly conserved residue in the TBC domain, and c.468C-A transversion, resulting in a cys156-to-ter substitution (C156X; 613577.0006). The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, were not present in several large exome databases and segregated with the disorder in the family. The patients developed clonic seizures early in the second month of life and thereafter developed prolonged, almost continuous seizures of different types with severe neurologic deterioration and lack of psychomotor development. The clinical diagnosis was consistent with malignant migrating partial seizures of infancy (MMPSI). Coimmunoprecipitation studies showed that the F229S mutation impaired the interaction of TBC1D24 with ARF6 (600464), and overexpression of the mutant protein in primary cortical neurons abolished the ability of TBC1D24 to increase neurite length and arborization, consistent with a loss of function.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Division of Medical Genetics; Sainte-Justine Hospital, SCV000211977.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV004045864.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Nov 10, 2024