1-229431994-C-G

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_001100.4(ACTA1):c.808G>C(p.Gly270Arg) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/22 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G270C) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 31)
• Consequence: ACTA1 NM_001100.4 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 5.93

Genes affected

ACTA1 (HGNC:129): (actin alpha 1, skeletal muscle) The product encoded by this gene belongs to the actin family of proteins, which are highly conserved proteins that play a role in cell motility, structure and integrity. Alpha, beta and gamma actin isoforms have been identified, with alpha actins being a major constituent of the contractile apparatus, while beta and gamma actins are involved in the regulation of cell motility. This actin is an alpha actin that is found in skeletal muscle. Mutations in this gene cause a variety of myopathies, including nemaline myopathy, congenital myopathy with excess of thin myofilaments, congenital myopathy with cores, and congenital myopathy with fiber-type disproportion, diseases that lead to muscle fiber defects with manifestations such as hypotonia. [provided by RefSeq, Sep 2019]

ACMG classification

Verdict is Pathogenic. Variant got 19 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_001100.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-229431902-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 434074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant where missense usually causes diseases, ACTA1
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 1-229431994-C-G is Pathogenic according to our data. Variant chr1-229431994-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 228243.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-229431994-C-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTA1	NM_001100.4	c.808G>C	p.Gly270Arg	missense_variant, splice_region_variant	5/7	ENST00000366684.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTA1	ENST00000366684.7	c.808G>C	p.Gly270Arg	missense_variant, splice_region_variant	5/7	1	NM_001100.4	P1
ACTA1	ENST00000366683.4	c.808G>C	p.Gly270Arg	missense_variant, splice_region_variant	5/7	5
ACTA1	ENST00000684723.1	c.673G>C	p.Gly225Arg	missense_variant, splice_region_variant	4/6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Actin accumulation myopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jun 30, 2017

This sequence change replaces glycine with arginine at codon 270 of the ACTA1 protein (p.Gly270Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant also falls at the last nucleotide of exon 5 of the ACTA1 coding sequence, which is part of the consensus splice site for this exon. Nucleotide substitutions within the consensus splice site are relatively common causes of aberrant splicing (PMID: 17576681, 9536098). This variant is not present in population databases (ExAC no frequency). This variant has been reported in several individuals affected with nemaline myopathy (PMID: 12921789, 15226407, 21514153). This variant is also known as Gly268Arg in the literature. ClinVar contains an entry for this variant (Variation ID: 228243). Experimental studies do not agree on the impact of this missense change. One study reports this sequence change behaves similar to wild type (PMID: 17227580) while another study reports this change impairs polymerization (PMID: 15226407). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. A different missense substitution at this codon (p.Gly270Cys, also reported as p.Gly268Cys) has been determined to be pathogenic (PMID: 12921789, 15226407, 15198992, 11333380). This suggests that the glycine residue is critical for ACTA1 protein function and that other missense substitutions at this position may also be pathogenic. For these reasons, this variant has been classified as Pathogenic. -

Neuromuscular disease Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Dec 21, 2018

The p.Gly270Arg variant in ACTA1 (also known as p.Gly268Arg) has been previously reported in at least 4 individuals with nemaline myopathy, including 2 confirme d de novo occurrences (Sparrow 2003, Laing 2009, LMM data). It was absent from l arge population studies. Several different variants at this position have occurr ed de novo in children with nemaline myopathy (p.Gly270Asp, p.Gly270Cys, and p.G ly270Ser; reported as p.Gly268Asp, p.Gly268Cys, and p.Gly268Ser; Ilkovski 2001, Graziano 2004, Ohlsson 2004, Laing 2009), supporting that changes at this codon are not tolerated. In vitro functional studies and structural analysis of the pr otein support an impact on protein function (Costa 2004, Bathe 2007, von der Eck en 2015). In addition, this variant is located last three bases of the exon, whi ch is part of the 5? splice region and computational tools suggest a possible im pact to splicing. In summary, this variant meets criteria to be classified as pa thogenic for autosomal dominant nemaline myopathy. ACMG/AMP Criteria applied: P M5_Strong, PM6_Strong, PS4_Moderate, PS3_Moderate, PP3. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.56
Cadd	Pathogenic	34
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.97	D
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.98	D
M_CAP	Pathogenic	0.81	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	4.4	H
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-6.2	D
REVEL	Pathogenic	0.98
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.81
MutPred		0.91		Loss of glycosylation at S267 (P = 0.0472);
MVP		1.0
ClinPred		1.0	D
GERP RS		4.3
Varity_R		0.93
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.030		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: rs121909525; hg19: chr1-229567741;