rs58064122

Positions:

• chr17-44913334-G-A
• chr17-44913334-G-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_002055.5(GFAP):​c.715C>T​(p.Arg239Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R239P) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GFAP NM_002055.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9 O:2
• Conservation: PhyloP100: 6.27

Genes affected

GFAP (HGNC:4235): (glial fibrillary acidic protein) This gene encodes one of the major intermediate filament proteins of mature astrocytes. It is used as a marker to distinguish astrocytes from other glial cells during development. Mutations in this gene cause Alexander disease, a rare disorder of astrocytes in the central nervous system. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a region_of_interest Coil 2A (size 21) in uniprot entity GFAP_HUMAN there are 6 pathogenic changes around while only 1 benign (86%) in NM_002055.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr17-44913333-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 16168.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.991
• PP5: Variant 17-44913334-G-A is Pathogenic according to our data. Variant chr17-44913334-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 16167.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFAP	NM_002055.5	c.715C>T	p.Arg239Cys	missense_variant	4/9	ENST00000588735.3
GFAP	NM_001363846.2	c.715C>T	p.Arg239Cys	missense_variant	4/10
GFAP	NM_001242376.3	c.715C>T	p.Arg239Cys	missense_variant	4/7
GFAP	NM_001131019.3	c.715C>T	p.Arg239Cys	missense_variant	4/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFAP	ENST00000588735.3	c.715C>T	p.Arg239Cys	missense_variant	4/9	1	NM_002055.5	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Alexander disease Pathogenic:8 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	The GFAP c.715C>T (p.Arg239Cys) variant has been reported previously in association with Alexander disease (Li et al., 2002). Functional studies indicate R239C affects the stability of GFAP protein, altering the normal solubility and organization of GFAP networks, and leading to compromised glutamate transport in astrocytes (Hsia et al., 2005). The p.Arg239Cys variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been submitted to ClinVar as Pathogenic. The amino acid Arg at position 239 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Arg239Cys in GFAP is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 14, 2019	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 01, 2005	- -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	This recurrent pathogenic variant has been previously reported in multiple individuals with Alexander disease (PMID: 20301351, 26478912, 23364391, 11567214, 11138011, 11587071, 15732098, 34146839). Experimental evidence suggests that the c.715C>T (p.Arg239Cys) variant affects the stability of the GFAP protein and compromises glutamate transport in astrocytes (PMID: 20448479, 15840648). The c.715C>T (p.Arg239Cys) variant is absent from the gnomAD population database and thus is presumed to be rare. It affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.715C>T (p.Arg239Cys) variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 17, 2023	Variant summary: GFAP c.715C>T (p.Arg239Cys) results in a non-conservative amino acid change located in the Intermediate filament, rod domain (IPR039008) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251450 control chromosomes. c.715C>T has been reported in the literature in multiple individuals affected with Alexander Disease (examples: Brenner_2001, Rodriguez_2001). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence showing the variant is associated with impaired autophagy leading to abnormal GFAP protein accumulation in Alexander disease (Tang_2008). The following publications have been ascertained in the context of this evaluation (PMID: 11138011, 11567214, 18276609). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Feb 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Mar 26, 2021	The GFAP c.715C>T (p.Arg239Cys) variant is a missense variant that is well-described as a recurrent pathogenic variant in patients with infantile- and juvenile-onset Alexander disease (Srivastava et al. 2002). Across a selection of the available literature, the p.Arg239Cys variant has been identified in a heterozygous state in 14 individuals with Alexander disease, with symptom onset ranging from six months to seven years of age (Brenner et al. 2001; Rodriguez et al. 2001; Zang et al. 2013; Jany et al. 2015). When family studies were performed, the p.Arg239Cys variant was determined to have occurred de novo (Brenner et al. 2001; Rodriguez et al. 2001; Zang et al. 2013). While many patients with the p.Arg239Cys variant are described to have a severe phenotype, the reported clinical features are variable. Of the eight patients described in Brenner et al. (2001) and Rodriguez et al. (2001), three had macrocephaly (details were not provided for the other patients), three were alive with disease duration ranging from 1.5-6.5 years, and five were deceased with disease duration ranging from 3.5-10 years. In the cohort described by Jany et al. (2015), cognition ranged from normal to severe intellectual disability. Other reported variable features included failure to thrive, emesis, swallowing difficulties, dysarthria, urinary incontinence, gait deterioration, and intermittent ataxia, among others. The p.Arg239Cys variant was absent from two individuals with non-Alexander disease leukodystrophy and from 53 control individuals without neurologic disease (Brenner et al. 2001), and is not found in the Genome Aggregation Database despite good sequencing coverage, so the variant is presumed to be rare. The p.Arg239Cys variant has been shown to affect GFAP solubility and the organization of GFAP networks (Hsiao et al. 2005). Western blotting and whole-cell patch clamp recordings have also suggested that glutamate uptake is reduced in variant-expressing astrocytes (Tian et al. 2010). This effect may play an important role in the pathogenesis of neuronal and oligodendrocyte injury and death in Alexander disease, as neurons co-cultured with astrocytes expressing the variant protein exhibited higher rates of death following glutamate challenge. Based on the collective evidence, the p.Arg239Cys variant is classified as pathogenic for Alexander disease. -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and gain of function are suggested as mechanisms of disease in this gene and are associated with Alexander disease (MIM#203450). Functional studies have demonstrated both dominant negative and gain of function are possible mechanisms of disease, however, the latter is the most widely accepted mechanism (OMIM, GeneReviews, PMIDs: 11138011, 30355500, 31484723). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (DECIPHER, PMID: 19386454). (SP) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals with infantile and juvenile Alexander disease and is considered a recurrent variant (ClinVar, PMID: 19386454). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

not provided Pathogenic:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 27, 2017	The R239C pathogenic missense variant in the GFAP gene has been reported previously in association with Alexander disease (Brenner et al., 2001; Li et al., 2002). Functional studies indicate R239C affects the stability of GFAP protein, altering the normal solubility and organization of GFAP networks, and leading to compromised glutamate transport in astrocytes (Hsia et al., 2005; Tian et al., 2010). It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R239C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Additionally, this substitution occurs at a position that is conserved across species, and other missense mutations at the same position (R239G/H/P/L) have been reported in the Human Gene Mutation Database in association with Alexander disease (Stenson et al., 2014). -
not provided, no classification provided	literature only	Epithelial Biology; Institute of Medical Biology, Singapore	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.75
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.48
CADD	Pathogenic	34
DANN	Pathogenic	1.0
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D;D;D;D
M_CAP	Uncertain	0.16	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Uncertain	0.66	T
Polyphen		1.0	.;D;.;.;.;.;.;.
Vest4		0.95, 0.95, 0.96
MutPred		0.98		Gain of catalytic residue at Q241 (P = 0.0165);Gain of catalytic residue at Q241 (P = 0.0165);Gain of catalytic residue at Q241 (P = 0.0165);.;Gain of catalytic residue at Q241 (P = 0.0165);Gain of catalytic residue at Q241 (P = 0.0165);Gain of catalytic residue at Q241 (P = 0.0165);.;
MVP		0.99
MPC		1.4
ClinPred		1.0	D
GERP RS		4.9
Varity_R		0.95
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs58064122; hg19: chr17-42990702;