NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter) AND Ichthyosis vulgaris

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: May 4, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000490339.13

Allele description [Variation Report for NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter)]

NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter)

Genes:

CCDST:cervical cancer associated DHX9 suppressive transcript [Gene - HGNC]
FLG:filaggrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter)

HGVS:

NC_000001.11:g.152309169G>T
NG_016190.1:g.21035C>A
NM_002016.2:c.5717C>AMANE SELECT
NP_002007.1:p.Ser1906Ter
NP_002007.1:p.Ser1906Ter
LRG_1028t1:c.5717C>A
LRG_1028:g.21035C>A
LRG_1028p1:p.Ser1906Ter
NC_000001.10:g.152281645G>T
NM_002016.1:c.5717C>A

Protein change:

S1906*

Links:

dbSNP: rs141784184

NCBI 1000 Genomes Browser:

rs141784184

Molecular consequence:

NM_002016.2:c.5717C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Ichthyosis vulgaris
Synonyms:: Ichthyosis simplex; Dominant ichthyosis vulgaris
Identifiers:: MONDO: MONDO:0024304; MedGen: C0079584; OMIM: 146700

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267321	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2016)	germline	reference population	PubMed (3) [See all records that cite these PMIDs] 16550169, 16815158, 25741868
SCV001142307	Reproductive Health Research and Development, BGI Genomics	no assertion criteria provided	Pathogenic (Jan 6, 2020)	germline	curation
SCV002516387	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Pathogenic (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000267321

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2016)

germline

reference population

PubMed (3)
[See all records that cite these PMIDs]

SCV001142307

Reproductive Health Research and Development, BGI Genomics

no assertion criteria provided

Pathogenic
(Jan 6, 2020)

germline

curation

SCV002516387

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2019)

Pathogenic
(May 4, 2022)

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, curation
East Asian	germline	unknown	1	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

Common loss-of-function variants of the epidermal barrier protein filaggrin are a major predisposing factor for atopic dermatitis.

Palmer CN, Irvine AD, Terron-Kwiatkowski A, Zhao Y, Liao H, Lee SP, Goudie DR, Sandilands A, Campbell LE, Smith FJ, O'Regan GM, Watson RM, Cecil JE, Bale SJ, Compton JG, DiGiovanna JJ, Fleckman P, Lewis-Jones S, Arseculeratne G, Sergeant A, Munro CS, El Houate B, et al.

Nat Genet. 2006 Apr;38(4):441-6. Epub 2006 Mar 19.

PubMed [citation]

PMID:: 16550169

Loss-of-function variations within the filaggrin gene predispose for atopic dermatitis with allergic sensitizations.

Weidinger S, Illig T, Baurecht H, Irvine AD, Rodriguez E, Diaz-Lacava A, Klopp N, Wagenpfeil S, Zhao Y, Liao H, Lee SP, Palmer CN, Jenneck C, Maintz L, Hagemann T, Behrendt H, Ring J, Nothen MM, McLean WH, Novak N.

J Allergy Clin Immunol. 2006 Jul;118(1):214-9. Epub 2006 Jun 9. Erratum in: J Allergy Clin Immunol. 2006 Oct;118(4):922. J Allergy Clin Immunol. 2006 Sep;118(3):724.

PubMed [citation]

PMID:: 16815158

See all PubMed Citations (3)

Details of each submission

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267321.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	1	not provided	not provided	reference population	PubMed (3)

#	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		1	not provided	not provided	not provided

From Reproductive Health Research and Development, BGI Genomics, SCV001142307.1

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

Description

NM_002016.1:c.5717C>A in the FLG gene has an allele frequency of 0.013 in East Asia subpopulation in the gnomAD database.This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.5717C>A (p.Ser1906*) variant has been detected in a patient affected with ichthyosis vulgaris (PMID: 28407221). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PVS1; PM2_supporting; PP4.

#	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

From Mendelics, SCV002516387.1

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

#	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: Nov 10, 2024

ClinVar

Relating variation to medicine