NM_002055.5(GFAP):c.235C>A (p.Arg79Ser) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 11, 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:: RCV000056866.7

Allele description [Variation Report for NM_002055.5(GFAP):c.235C>A (p.Arg79Ser)]

NM_002055.5(GFAP):c.235C>A (p.Arg79Ser)

Gene:

GFAP:glial fibrillary acidic protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_002055.5(GFAP):c.235C>A (p.Arg79Ser)

HGVS:

NC_000017.11:g.44915252G>T
NG_008401.1:g.5295C>A
NM_001131019.3:c.235C>A
NM_001242376.3:c.235C>A
NM_001363846.2:c.235C>A
NM_002055.5:c.235C>AMANE SELECT
NP_001124491.1:p.Arg79Ser
NP_001229305.1:p.Arg79Ser
NP_001350775.1:p.Arg79Ser
NP_002046.1:p.Arg79Ser
NC_000017.10:g.42992620G>T
NM_002055.4:c.235C>A

Protein change:

R79S

Links:

dbSNP: rs59793293

NCBI 1000 Genomes Browser:

rs59793293

Molecular consequence:

NM_001131019.3:c.235C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001242376.3:c.235C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363846.2:c.235C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002055.5:c.235C>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000087979	Epithelial Biology; Institute of Medical Biology, Singapore	no classification provided	not provided	not provided	not provided
SCV002303110	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 11, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 11138011, 18584981, 23254569, 28882119, 21917775, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000087979

Epithelial Biology; Institute of Medical Biology, Singapore

no classification provided

not provided

SCV002303110

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 11, 2022)

germline

clinical testing

PubMed (6)
[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
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

Mutations in GFAP, encoding glial fibrillary acidic protein, are associated with Alexander disease.

Brenner M, Johnson AB, Boespflug-Tanguy O, Rodriguez D, Goldman JE, Messing A.

Nat Genet. 2001 Jan;27(1):117-20.

PubMed [citation]

PMID:: 11138011

Tumor-like enlargement of the optic chiasm in an infant with Alexander disease.

Mignot C, Desguerre I, Burglen L, Hertz-Pannier L, Renaldo F, Gadisseux JF, Gallet S, Pham-Dinh D, Boespflug-Tanguy O, Rodriguez D.

Brain Dev. 2009 Mar;31(3):244-7. doi: 10.1016/j.braindev.2008.05.005. Epub 2008 Jun 26.

PubMed [citation]

PMID:: 18584981

See all PubMed Citations (6)

Details of each submission

From Epithelial Biology; Institute of Medical Biology, Singapore, SCV000087979.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	not provided	not provided	1	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002303110.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

ClinVar contains an entry for this variant (Variation ID: 66469). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant disrupts the p.Arg79 amino acid residue in GFAP. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11138011, 18584981, 23254569, 28882119). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This missense change has been observed in individual(s) with Alexander disease (PMID: 21917775). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 79 of the GFAP protein (p.Arg79Ser).

#	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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