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NM_001199107.2(TBC1D24):c.493G>A (p.Gly165Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jul 16, 2021)
Last evaluated:
Nov 4, 2020
Accession:
VCV000207484.9
Variation ID:
207484
Description:
single nucleotide variant
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NM_001199107.2(TBC1D24):c.493G>A (p.Gly165Ser)

Allele ID
203230
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2496641 (GRCh38) GRCh38 UCSC
16: 2546642 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.2496641G>A
NC_000016.9:g.2546642G>A
NG_028170.1:g.26496G>A
... more HGVS
Protein change
G165S
Other names
p.G165S:GGC>AGC
Canonical SPDI
NC_000016.10:2496640:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00066
1000 Genomes Project 0.00080
The Genome Aggregation Database (gnomAD) 0.00127
The Genome Aggregation Database (gnomAD), exomes 0.00062
Trans-Omics for Precision Medicine (TOPMed) 0.00148
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00171
Links
ClinGen: CA318989
dbSNP: rs200926225
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Feb 9, 2016 RCV000189669.7
Likely benign 1 criteria provided, single submitter Nov 4, 2020 RCV000466794.5
Uncertain significance 1 criteria provided, single submitter Sep 6, 2016 RCV000660402.1
Likely benign 1 criteria provided, single submitter Oct 11, 2018 RCV000716688.1
Likely benign 1 criteria provided, single submitter Jul 31, 2020 RCV001535427.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TBC1D24 - - GRCh38
GRCh37
619 664

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Feb 09, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000269863.3
Submitted: (Mar 21, 2019)
Evidence details
Comment:
p.Gly165Ser in exon 2 of TBC1D24: This variant is not expected to have clinical significance because it has been identified in 0.5% (51/9574) of African … (more)
Likely benign
(Jul 31, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000243315.12
Submitted: (Jul 16, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 24291220)
Uncertain significance
(Sep 06, 2016)
criteria provided, single submitter
Method: clinical testing
Early infantile epileptic encephalopathy 16
Allele origin: paternal
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000782484.1
Submitted: (Feb 28, 2018)
Evidence details
Likely benign
(Oct 11, 2018)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847531.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
In silico models in agreement (benign) ;Sub-population frequency in support of benign classification (not ava blue, manual h-w)
Likely benign
(Nov 04, 2020)
criteria provided, single submitter
Method: clinical testing
Caused by mutation in the TBC1 domain family, member 24
Epileptic encephalopathy, early infantile, 1
Deafness, autosomal dominant 65
Allele origin: germline
Invitae
Accession: SCV000560540.6
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs200926225...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 20, 2021