rs28999111

chr17-81512000-G-Achr17-81512000-G-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1 PM2 PP2 PP3_Strong PP5

The NM_001614.5(ACTG1):c.266C>T(p.Thr89Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. T89T) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ACTG1 NM_001614.5 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.44

Genes affected

ACTG1 (HGNC:144): (actin gamma 1) Actins are highly conserved proteins that are involved in various types of cell motility and in maintenance of the cytoskeleton. Three main groups of actin isoforms have been identified in vertebrate animals: alpha, beta, and gamma. The alpha actins are found in muscle tissues and are a major constituent of the contractile apparatus. The beta and gamma actins co-exist in most cell types as components of the cytoskeleton and as mediators of internal cell motility. Actin gamma 1, encoded by this gene, is a cytoplasmic actin found in all cell types. Mutations in this gene are associated with DFNA20/26, a subtype of autosomal dominant non-syndromic sensorineural progressive hearing loss and also with Baraitser-Winter syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM1: In a turn (size 3) in uniprot entity ACTG_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_001614.5
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, ACTG1
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.962
• PP5: Variant 17-81512000-G-A is Pathogenic according to our data. Variant chr17-81512000-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 18315.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr17-81512000-G-A is described in Lovd as [Likely_pathogenic]. Variant chr17-81512000-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACTG1	NM_001614.5	c.266C>T	p.Thr89Ile	missense_variant	3/6	ENST00000573283.7
ACTG1	NM_001199954.3	c.266C>T	p.Thr89Ile	missense_variant	3/6
ACTG1	NR_037688.3	n.338C>T		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACTG1	ENST00000573283.7	c.266C>T	p.Thr89Ile	missense_variant	3/6	5	NM_001614.5	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461748 Hom.: 0 Cov.: 37 AF XY: 0.00000138 AC XY: 1 AN XY: 727172

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Autosomal dominant nonsyndromic hearing loss 20 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Nov 01, 2003

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
Cadd	Uncertain	25
Dann	Benign	0.72
DEOGEN2	Pathogenic	0.89	D;D;D;D;D;D;D;D;D;D;.
Eigen	Benign	-0.078
Eigen_PC	Benign	-0.045
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Pathogenic	0.77	D
MetaRNN	Pathogenic	0.96	D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.82	D
MutationAssessor	Uncertain	2.6	M;M;M;M;M;M;.;.;.;.;.
MutationTaster	Benign	1.0	A;A;A;A;A
PrimateAI	Pathogenic	0.84	D
Sift4G	Uncertain	0.052	T;T;T;T;T;.;.;.;T;T;T
Polyphen		0.0010	B;B;B;B;B;B;.;.;.;.;.
Vest4		0.90
MutPred		0.80		Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);.;Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);Gain of catalytic residue at L94 (P = 0.1045);
MVP		0.94
ClinPred		0.98	D
GERP RS		3.0
Varity_R		0.96
gMVP		0.94

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: rs28999111; hg19: chr17-79479026;