NM_001199107.2(TBC1D24):c.229ATCGTGGGCAAG[1] (p.77IVGK[1]) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 18, 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:: RCV001044367.13

Allele description [Variation Report for NM_001199107.2(TBC1D24):c.229ATCGTGGGCAAG[1] (p.77IVGK[1])]

NM_001199107.2(TBC1D24):c.229ATCGTGGGCAAG[1] (p.77IVGK[1])

Gene:

TBC1D24:TBC1 domain family member 24 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_001199107.2(TBC1D24):c.229ATCGTGGGCAAG[1] (p.77IVGK[1])

HGVS:

NC_000016.10:g.2496377ATCGTGGGCAAG[1]
NG_028170.1:g.26232ATCGTGGGCAAG[1]
NM_001199107.2:c.229ATCGTGGGCAAG[1]MANE SELECT
NM_020705.3:c.229ATCGTGGGCAAG[1]
NP_001186036.1:p.77IVGK[1]
NP_065756.1:p.77IVGK[1]
NC_000016.9:g.2546378ATCGTGGGCAAG[1]
NC_000016.9:g.2546378_2546389del
NM_001199107.1:c.241_252del
NM_001199107.1:c.241_252del12
NM_001199107.1:c.241_252delATCGTGGGCAAG
NM_001199107.2:c.241_252delMANE SELECT

Links:

OMIM: 613577.0017; dbSNP: rs761918906

NCBI 1000 Genomes Browser:

rs761918906

Molecular consequence:

NM_001199107.2:c.229ATCGTGGGCAAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_020705.3:c.229ATCGTGGGCAAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 1 (DEE1)
Synonyms:: INFANTILE SPASM SYNDROME, X-LINKED 1; X-linked infantile spasms; West's syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010632; MedGen: C3463992; OMIM: 308350

Name:: Autosomal dominant nonsyndromic hearing loss 65
Synonyms:: Deafness, autosomal dominant 65
Identifiers:: MONDO: MONDO:0014470; MedGen: C3892048; Orphanet: 90635; OMIM: 616044

Name:: Caused by mutation in the TBC1 domain family, member 24
Identifiers:: MedGen: CN236805

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001208161	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 18, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 29416524, 31112829, 31257402, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001208161

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 18, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Homozygous TBC1D24 Mutation in a Case of Epilepsia Partialis Continua.

Zhou Q, Lin Y, Ye J, Li L, Hu N, Wang D, Wang Y.

Front Neurol. 2017;8:750. doi: 10.3389/fneur.2017.00750.

PubMed [citation]

PMID:: 29416524
PMCID:: PMC5787533

Infantile epilepsy with multifocal myoclonus caused by TBC1D24 mutations.

Zhang J, Chen J, Zeng Q, Zhang L, Tian X, Yang X, Yang Z, Wu Y, Wu X, Zhang Y.

Seizure. 2019 Jul;69:228-234. doi: 10.1016/j.seizure.2019.05.010. Epub 2019 May 13.

PubMed [citation]

PMID:: 31112829

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001208161.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant, c.241_252del, results in the deletion of 4 amino acid(s) of the TBC1D24 protein (p.Ile81_Lys84del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs761918906, gnomAD 0.1%). This variant has been observed in individual(s) with clinical features of TBC1D24-related conditions (PMID: 29416524, 31112829, 31257402). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.229_240del (p.82_84del). ClinVar contains an entry for this variant (Variation ID: 418692). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 10, 2024

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