NM_000268.4(NF2):c.30del (p.Phe11fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 4, 2019
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:: RCV001009248.1

Allele description [Variation Report for NM_000268.4(NF2):c.30del (p.Phe11fs)]

NM_000268.4(NF2):c.30del (p.Phe11fs)

Gene:

NF2:NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q12.2

Genomic location:

Preferred name:

NM_000268.4(NF2):c.30del (p.Phe11fs)

HGVS:

NC_000022.11:g.29604028del
NG_009057.1:g.5473del
NM_000268.4:c.30delMANE SELECT
NM_016418.5:c.30del
NM_181825.3:c.30del
NM_181828.3:c.30del
NM_181829.3:c.30del
NM_181830.3:c.30del
NM_181831.3:c.30del
NM_181832.3:c.30del
NM_181833.3:c.30del
NP_000259.1:p.Phe11fs
NP_057502.2:p.Phe11fs
NP_861546.1:p.Phe11fs
NP_861966.1:p.Phe11fs
NP_861967.1:p.Phe11fs
NP_861968.1:p.Phe11fs
NP_861969.1:p.Phe11fs
NP_861970.1:p.Phe11fs
NP_861971.1:p.Phe11fs
LRG_511t1:c.30del
LRG_511t2:c.30del
LRG_511:g.5473del
LRG_511p2:p.Phe11fs
NC_000022.10:g.30000017del
NM_000268.3:c.30delC
NR_156186.2:n.396del

Protein change:

F11fs

Links:

dbSNP: rs1601515836

NCBI 1000 Genomes Browser:

rs1601515836

Molecular consequence:

NM_000268.4:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016418.5:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181825.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181828.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181829.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181830.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181831.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181832.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_181833.3:c.30del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_156186.2:n.396del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001169069	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Feb 4, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001169069

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Feb 4, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001169069.1

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

Description

The c.30delC variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is not observed in large population cohorts (Lek et al., 2016). It causes a frameshift starting with codon Phenylalanine 11, changes this amino acid to a Serine residue and creates a premature Stop codon at position 14 of the new reading frame, denoted p.Phe11SerfsX14. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. We interpret this variant as pathogenic.

#	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 5, 2022

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