chr7-30612212-A-C

Position:

• chr7-30612212-A-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PM5 PP3_Strong PP5_Moderate

The NM_002047.4(GARS1):​c.998A>C​(p.Glu333Ala) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E333D) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GARS1 NM_002047.4 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.22

Genes affected

GARS1 (HGNC:4162): (glycyl-tRNA synthetase 1) This gene encodes glycyl-tRNA synthetase, one of the aminoacyl-tRNA synthetases that charge tRNAs with their cognate amino acids. The encoded enzyme is an (alpha)2 dimer which belongs to the class II family of tRNA synthetases. It has been shown to be a target of autoantibodies in the human autoimmune diseases, polymyositis or dermatomyositis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

GARS1 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-30612213-G-C is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.992
• PP5: Variant 7-30612212-A-C is Pathogenic according to our data. Variant chr7-30612212-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 423476.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GARS1	NM_002047.4	c.998A>C	p.Glu333Ala	missense_variant	8/17	ENST00000389266.8	NP_002038.2
GARS1	NM_001316772.1	c.836A>C	p.Glu279Ala	missense_variant	8/17		NP_001303701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GARS1	ENST00000389266.8	c.998A>C	p.Glu333Ala	missense_variant	8/17	1	NM_002047.4	ENSP00000373918.3
GARS1	ENST00000675651.1	c.998A>C	p.Glu333Ala	missense_variant	8/17			ENSP00000502513.1
GARS1	ENST00000675810.1	c.896A>C	p.Glu299Ala	missense_variant	7/16			ENSP00000502743.1
GARS1	ENST00000675693.1	c.830A>C	p.Glu277Ala	missense_variant	9/18			ENSP00000502174.1
GARS1	ENST00000675051.1	c.797A>C	p.Glu266Ala	missense_variant	8/17			ENSP00000502296.1
GARS1	ENST00000674815.1	c.629A>C	p.Glu210Ala	missense_variant	8/17			ENSP00000502799.1
GARS1	ENST00000674851.1	c.629A>C	p.Glu210Ala	missense_variant	9/18			ENSP00000502451.1
GARS1	ENST00000444666.6	n.998A>C		non_coding_transcript_exon_variant	8/18	3		ENSP00000415447.2
GARS1	ENST00000674616.1	n.*712A>C		non_coding_transcript_exon_variant	9/18			ENSP00000502408.1
GARS1	ENST00000674643.1	n.998A>C		non_coding_transcript_exon_variant	8/17			ENSP00000501636.1
GARS1	ENST00000674737.1	n.*336A>C		non_coding_transcript_exon_variant	9/18			ENSP00000502464.1
GARS1	ENST00000674807.1	n.998A>C		non_coding_transcript_exon_variant	8/16			ENSP00000502814.1
GARS1	ENST00000675529.1	n.*868A>C		non_coding_transcript_exon_variant	9/18			ENSP00000501655.1
GARS1	ENST00000675859.1	n.998A>C		non_coding_transcript_exon_variant	8/15			ENSP00000502033.1
GARS1	ENST00000676088.1	n.*940A>C		non_coding_transcript_exon_variant	10/19			ENSP00000501884.1
GARS1	ENST00000676140.1	n.998A>C		non_coding_transcript_exon_variant	8/17			ENSP00000502571.1
GARS1	ENST00000676164.1	n.*449A>C		non_coding_transcript_exon_variant	8/17			ENSP00000501986.1
GARS1	ENST00000676210.1	n.*287A>C		non_coding_transcript_exon_variant	9/18			ENSP00000502373.1
GARS1	ENST00000676259.1	n.*430A>C		non_coding_transcript_exon_variant	8/17			ENSP00000501980.1
GARS1	ENST00000676403.1	n.998A>C		non_coding_transcript_exon_variant	8/16			ENSP00000502681.1
GARS1	ENST00000674616.1	n.*712A>C		3_prime_UTR_variant	9/18			ENSP00000502408.1
GARS1	ENST00000674737.1	n.*336A>C		3_prime_UTR_variant	9/18			ENSP00000502464.1
GARS1	ENST00000675529.1	n.*868A>C		3_prime_UTR_variant	9/18			ENSP00000501655.1
GARS1	ENST00000676088.1	n.*940A>C		3_prime_UTR_variant	10/19			ENSP00000501884.1
GARS1	ENST00000676164.1	n.*449A>C		3_prime_UTR_variant	8/17			ENSP00000501986.1
GARS1	ENST00000676210.1	n.*287A>C		3_prime_UTR_variant	9/18			ENSP00000502373.1
GARS1	ENST00000676259.1	n.*430A>C		3_prime_UTR_variant	8/17			ENSP00000501980.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Feb 17, 2017

A variant that is likely pathogenic has been identified in the GARS gene. The E333A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. A different amino acid substitution at the same codon (E333D) was previously identified in multiple family members affected with CMT2D (Sun et al., 2015). The E333A variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The E333A 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. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.47
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.96
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Pathogenic	1.0	D
M_CAP	Pathogenic	0.74	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.0	D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Pathogenic	-5.5	D
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.98
MutPred		0.91		Gain of MoRF binding (P = 0.0256);
MVP		0.97
MPC		1.2
ClinPred		1.0	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.98
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: rs863224873; hg19: chr7-30651828;