NM_001371596.2(MFSD8):c.1040dup (p.Trp348fs) AND Neuronal ceroid lipofuscinosis 7

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 16, 2018
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:: RCV000779430.6

Allele description [Variation Report for NM_001371596.2(MFSD8):c.1040dup (p.Trp348fs)]

NM_001371596.2(MFSD8):c.1040dup (p.Trp348fs)

Gene:

MFSD8:major facilitator superfamily domain containing 8 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4q28.2

Genomic location:

Preferred name:

NM_001371596.2(MFSD8):c.1040dup (p.Trp348fs)

HGVS:

NC_000004.12:g.127921922dup
NG_008657.1:g.49063dup
NM_001363520.3:c.839dup
NM_001363521.3:c.725dup
NM_001371590.2:c.905dup
NM_001371591.2:c.1040dup
NM_001371592.2:c.1046dup
NM_001371593.2:c.926dup
NM_001371594.2:c.893dup
NM_001371595.1:c.758dup
NM_001371596.2:c.1040dupMANE SELECT
NM_001410765.1:c.590dup
NM_152778.4:c.1040dup
NP_001350449.1:p.Trp281Metfs
NP_001350449.1:p.Trp281fs
NP_001350450.1:p.Trp243Metfs
NP_001350450.1:p.Trp243fs
NP_001358519.1:p.Trp303Metfs
NP_001358519.1:p.Trp303fs
NP_001358520.1:p.Trp348Metfs
NP_001358520.1:p.Trp348fs
NP_001358521.1:p.Trp350Metfs
NP_001358521.1:p.Trp350fs
NP_001358522.1:p.Trp310Metfs
NP_001358522.1:p.Trp310fs
NP_001358523.1:p.Trp299Metfs
NP_001358523.1:p.Trp299fs
NP_001358524.1:p.Trp254fs
NP_001358525.1:p.Trp348fs
NP_001397694.1:p.Trp198Metfs
NP_689991.1:p.Trp348fs
LRG_833t1:c.1040dup
LRG_833t2:c.1040dup
LRG_833:g.49063dup
LRG_833p1:p.Trp348fs
LRG_833p2:p.Trp348fs
NC_000004.11:g.128843077dup
NM_001363520.2:c.839dup
NM_001363521.2:c.725dup
NM_001371590.1:c.905dup
NM_001371591.1:c.1040dup
NM_001371592.1:c.1046dup
NM_001371593.1:c.926dup
NM_001371594.1:c.893dup
NM_152778.2:c.1040dupT

Protein change:

W243fs

Links:

dbSNP: rs1560718555

NCBI 1000 Genomes Browser:

rs1560718555

Molecular consequence:

NM_001363520.3:c.839dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001363521.3:c.725dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371590.2:c.905dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371591.2:c.1040dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371592.2:c.1046dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371593.2:c.926dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371594.2:c.893dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371595.1:c.758dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371596.2:c.1040dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001410765.1:c.590dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_152778.4:c.1040dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neuronal ceroid lipofuscinosis 7 (CLN7)
Synonyms:: MFSD8-Related Neuronal Ceroid-Lipofuscinosis
Identifiers:: MONDO: MONDO:0012588; MedGen: C1838571; Orphanet: 168491; Orphanet: 228366; OMIM: 610951

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000916046	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019)	Uncertain significance (Oct 16, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000916046

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)

Uncertain significance
(Oct 16, 2018)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000916046.1

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

Description

This variant results in a frameshift and is predicted to result in premature termination of the protein. It was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018) and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score for this variant, it could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene and cDNA change, and amino acid change. No publications were found based on this search. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for this disease.

#	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: Apr 9, 2023

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