NM_002047.4:c.548T>C

Variant names:

• chr7-30601179-T-C
• rs137852644
• NM_002047.4:c.548T>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.548T>C​(p.Leu183Pro) 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. 12/20 in silico tools predict a damaging 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. L183F) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GARS1 NM_002047.4 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:2 U:2 O:1
• Conservation: PhyloP100: 7.93

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]

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 chr7-30601178-C-T is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant 7-30601179-T-C is Pathogenic according to our data. Variant chr7-30601179-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 9205.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-30601179-T-C is described in Lovd as [Pathogenic]. Variant chr7-30601179-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GARS1	NM_002047.4	c.548T>C	p.Leu183Pro	missense_variant	Exon 4 of 17	ENST00000389266.8	NP_002038.2
GARS1	NM_001316772.1	c.386T>C	p.Leu129Pro	missense_variant	Exon 4 of 17		NP_001303701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GARS1	ENST00000389266.8	c.548T>C	p.Leu183Pro	missense_variant	Exon 4 of 17	1	NM_002047.4	ENSP00000373918.3
GARS1	ENST00000675651.1	c.548T>C	p.Leu183Pro	missense_variant	Exon 4 of 17			ENSP00000502513.1
GARS1	ENST00000675810.1	c.446T>C	p.Leu149Pro	missense_variant	Exon 3 of 16			ENSP00000502743.1
GARS1	ENST00000675693.1	c.380T>C	p.Leu127Pro	missense_variant	Exon 5 of 18			ENSP00000502174.1
GARS1	ENST00000675051.1	c.347T>C	p.Leu116Pro	missense_variant	Exon 4 of 17			ENSP00000502296.1
GARS1	ENST00000674815.1	c.179T>C	p.Leu60Pro	missense_variant	Exon 4 of 17			ENSP00000502799.1
GARS1	ENST00000674851.1	c.179T>C	p.Leu60Pro	missense_variant	Exon 5 of 18			ENSP00000502451.1
GARS1	ENST00000444666.6	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 18	3		ENSP00000415447.2
GARS1	ENST00000674616.1	n.*262T>C		non_coding_transcript_exon_variant	Exon 5 of 18			ENSP00000502408.1
GARS1	ENST00000674643.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 17			ENSP00000501636.1
GARS1	ENST00000674737.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 18			ENSP00000502464.1
GARS1	ENST00000674807.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 16			ENSP00000502814.1
GARS1	ENST00000675529.1	n.*418T>C		non_coding_transcript_exon_variant	Exon 5 of 18			ENSP00000501655.1
GARS1	ENST00000675859.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 15			ENSP00000502033.1
GARS1	ENST00000676088.1	n.*418T>C		non_coding_transcript_exon_variant	Exon 5 of 19			ENSP00000501884.1
GARS1	ENST00000676140.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 17			ENSP00000502571.1
GARS1	ENST00000676164.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 17			ENSP00000501986.1
GARS1	ENST00000676210.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 18			ENSP00000502373.1
GARS1	ENST00000676259.1	n.478T>C		non_coding_transcript_exon_variant	Exon 4 of 17			ENSP00000501980.1
GARS1	ENST00000676403.1	n.548T>C		non_coding_transcript_exon_variant	Exon 4 of 16			ENSP00000502681.1
GARS1	ENST00000674616.1	n.*262T>C		3_prime_UTR_variant	Exon 5 of 18			ENSP00000502408.1
GARS1	ENST00000675529.1	n.*418T>C		3_prime_UTR_variant	Exon 5 of 18			ENSP00000501655.1
GARS1	ENST00000676088.1	n.*418T>C		3_prime_UTR_variant	Exon 5 of 19			ENSP00000501884.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00152 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2 Uncertain:2 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

Charcot-Marie-Tooth disease type 2D Uncertain:1 Other:1

Jan 06, 2016

Inherited Neuropathy Consortium Ii, University Of Miami

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

GARS1-HMSN (exclusively dSMA-V) [Antonellis et al 2003, He et al 2015] -

not provided Pathogenic:1

Dec 01, 2020

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Neuronopathy, distal hereditary motor, type 5A Pathogenic:1

May 01, 2003

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Charcot-Marie-Tooth disease Uncertain:1

Aug 14, 2019

Genesis Genome Database

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	31
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.80	D
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.91
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Uncertain	0.56	D
PrimateAI	Pathogenic	0.89	D
PROVEAN	Pathogenic	-6.8	D
REVEL	Pathogenic	0.86
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.98
MutPred		0.96		Gain of disorder (P = 0.0222);
MVP		0.76
MPC		1.4
ClinPred		1.0	D
GERP RS		5.8
Varity_R		0.97
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs137852644; hg19: chr7-30640795;