NM_152468.5(TMC8):c.316del (p.Ile106fs) AND Epidermodysplasia verruciformis

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 8, 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:: RCV003759984.1

Allele description [Variation Report for NM_152468.5(TMC8):c.316del (p.Ile106fs)]

NM_152468.5(TMC8):c.316del (p.Ile106fs)

Genes:

LOC130061793:ATAC-STARR-seq lymphoblastoid silent region 9044 [Gene]
TMC6:transmembrane channel like 6 [Gene - OMIM - HGNC]
TMC8:transmembrane channel like 8 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_152468.5(TMC8):c.316del (p.Ile106fs)

HGVS:

NC_000017.11:g.78132376del
NG_007879.1:g.5033del
NG_007881.1:g.6599del
NG_196912.1:g.388del
NM_007267.7:c.-109del
NM_152468.5:c.316delMANE SELECT
NP_689681.2:p.Ile106Phefs
NP_689681.2:p.Ile106fs
LRG_118t1:c.-110del
LRG_119t1:c.316del
LRG_118:g.5033del
LRG_119:g.6599del
LRG_119p1:p.Ile106Phefs
NC_000017.10:g.76128456del
NC_000017.10:g.76128457del
NM_007267.6:c.-110delT
NM_152468.4:c.316delA

Protein change:

I106fs

Molecular consequence:

NM_007267.7:c.-109del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_152468.5:c.316del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Epidermodysplasia verruciformis
Identifiers:: MONDO: MONDO:0009176; MedGen: C0014522; OMIM: PS226400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004377078	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 8, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12426567, 22158547, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004377078

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 8, 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

Mutations in two adjacent novel genes are associated with epidermodysplasia verruciformis.

Ramoz N, Rueda LA, Bouadjar B, Montoya LS, Orth G, Favre M.

Nat Genet. 2002 Dec;32(4):579-81. Epub 2002 Nov 11.

PubMed [citation]

PMID:: 12426567

Lack of EVER2 protein in two epidermodysplasia verruciformis patients with skin cancer presenting previously unreported homozygous genetic deletions in the EVER2 gene.

Landini MM, Zavattaro E, Borgogna C, Azzimonti B, De Andrea M, Colombo E, Marenco F, Amantea A, Landolfo S, Gariglio M.

J Invest Dermatol. 2012 Apr;132(4):1305-8. doi: 10.1038/jid.2011.399. Epub 2011 Dec 8. No abstract available.

PubMed [citation]

PMID:: 22158547

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004377078.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TMC8-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ile106Phefs*17) in the TMC8 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TMC8 are known to be pathogenic (PMID: 12426567, 22158547).

#	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: May 19, 2024

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