NM_016495.6(TBC1D7):c.322dup (p.Tyr108fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 5, 2022
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:: RCV002958097.2

Allele description [Variation Report for NM_016495.6(TBC1D7):c.322dup (p.Tyr108fs)]

NM_016495.6(TBC1D7):c.322dup (p.Tyr108fs)

Genes:

TBC1D7:TBC1 domain family member 7 [Gene - OMIM - HGNC]
TBC1D7-LOC100130357:TBC1D7-LOC100130357 readthrough [Gene]

Variant type:

Duplication

Cytogenetic location:

6p24.1

Genomic location:

Preferred name:

NM_016495.6(TBC1D7):c.322dup (p.Tyr108fs)

HGVS:

NC_000006.12:g.13320967dup
NG_033862.1:g.12617dup
NM_001143964.4:c.322dup
NM_001143965.4:c.322dup
NM_001143966.4:c.241dup
NM_001258457.3:c.322dup
NM_001318805.2:c.322dup
NM_001318806.2:c.241dup
NM_001318809.2:c.322dup
NM_016495.6:c.322dupMANE SELECT
NP_001137436.1:p.Tyr108fs
NP_001137437.1:p.Tyr108fs
NP_001137438.1:p.Tyr81fs
NP_001245386.1:p.Tyr108fs
NP_001305734.1:p.Tyr108fs
NP_001305735.1:p.Tyr81fs
NP_001305738.1:p.Tyr108fs
NP_057579.1:p.Tyr108fs
NC_000006.11:g.13321198_13321199insA
NC_000006.11:g.13321199dup
NM_001143965.4:c.322dupT
NR_134872.2:n.412dup

Protein change:

Y108fs

Molecular consequence:

NM_001143964.4:c.322dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001143965.4:c.322dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001143966.4:c.241dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258457.3:c.322dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318805.2:c.322dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318806.2:c.241dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001318809.2:c.322dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016495.6:c.322dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_134872.2:n.412dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003272782	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 5, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23687350, 24515783, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003272782

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 5, 2022)

germline

clinical testing

PubMed (3)
[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

Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly.

Capo-Chichi JM, Tcherkezian J, Hamdan FF, Décarie JC, Dobrzeniecka S, Patry L, Nadon MA, Mucha BE, Major P, Shevell M, Bencheikh BO, Joober R, Samuels ME, Rouleau GA, Roux PP, Michaud JL.

J Med Genet. 2013 Nov;50(11):740-4. doi: 10.1136/jmedgenet-2013-101680. Epub 2013 May 17.

PubMed [citation]

PMID:: 23687350

TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease.

Alfaiz AA, Micale L, Mandriani B, Augello B, Pellico MT, Chrast J, Xenarios I, Zelante L, Merla G, Reymond A.

Hum Mutat. 2014 Apr;35(4):447-51. doi: 10.1002/humu.22529.

PubMed [citation]

PMID:: 24515783

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003272782.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Tyr108Leufs*24) in the TBC1D7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TBC1D7 are known to be pathogenic (PMID: 23687350, 24515783). This variant is present in population databases (rs758759342, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with TBC1D7-related conditions. 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: Sep 29, 2024

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