NM_001199107.2(TBC1D24):c.724C>T (p.Arg242Cys) AND Developmental and epileptic encephalopathy, 16

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: May 10, 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:: RCV000585843.10

Allele description [Variation Report for NM_001199107.2(TBC1D24):c.724C>T (p.Arg242Cys)]

NM_001199107.2(TBC1D24):c.724C>T (p.Arg242Cys)

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.724C>T (p.Arg242Cys)

Other names:

p.R242C:CGC>TGC

HGVS:

NC_000016.10:g.2496872C>T
NG_028170.1:g.26727C>T
NM_001199107.1:c.[724C>T]
NM_001199107.2:c.724C>TMANE SELECT
NM_020705.3:c.724C>T
NP_001186036.1:p.Arg242Cys
NP_001186036.1:p.Arg242Cys
NP_065756.1:p.Arg242Cys
NC_000016.9:g.2546873C>T
NM_001199107.1:c.724C>T
NM_001199107.1:c.[724C>T]
NM_001199107.2:c.724C>T
NM_020705.2:c.724C>T
Q9ULP9:p.Arg242Cys

Protein change:

R242C; ARG242CYS

Links:

UniProtKB: Q9ULP9#VAR_070915; OMIM: 613577.0007; dbSNP: rs398122965

NCBI 1000 Genomes Browser:

rs398122965

Molecular consequence:

NM_001199107.2:c.724C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020705.3:c.724C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000693777	NeuroMeGen, Hospital Clinico Santiago de Compostela	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 1, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002512332	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 10, 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

SCV000693777

NeuroMeGen, Hospital Clinico Santiago de Compostela

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 1, 2018)

germline

clinical testing

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

SCV002512332

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 10, 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	yes	1	not provided	not provided	1	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 NeuroMeGen, Hospital Clinico Santiago de Compostela, SCV000693777.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV002512332.1

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

Description

ACMG classification criteria: PS3 supporting, PS4 moderate, PM2 moderate, PM3 strong, PP3 supporting

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

Last Updated: Nov 10, 2024

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