NM_002161.6(IARS1):c.2422C>G (p.Arg808Gly) AND Growth retardation, intellectual developmental disorder, hypotonia, and hepatopathy

Germline classification:: Uncertain significance (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003340519.2

Allele description [Variation Report for NM_002161.6(IARS1):c.2422C>G (p.Arg808Gly)]

NM_002161.6(IARS1):c.2422C>G (p.Arg808Gly)

Gene:

IARS1:isoleucyl-tRNA synthetase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q22.31

Genomic location:

Preferred name:

NM_002161.6(IARS1):c.2422C>G (p.Arg808Gly)

HGVS:

NC_000009.12:g.92250720G>C
NG_051498.1:g.48037C>G
NG_116729.1:g.334G>C
NM_001374299.1:c.2347C>G
NM_001374300.1:c.2347C>G
NM_001374301.1:c.2338C>G
NM_001378569.1:c.2485C>G
NM_001378571.1:c.2443C>G
NM_001378572.1:c.2422C>G
NM_001378573.1:c.2422C>G
NM_001378574.1:c.2422C>G
NM_001378575.1:c.2422C>G
NM_001378576.1:c.2422C>G
NM_001378577.1:c.2422C>G
NM_001378578.1:c.2422C>G
NM_001378579.1:c.2422C>G
NM_001378580.1:c.2422C>G
NM_001378582.1:c.2326C>G
NM_001378583.1:c.2299C>G
NM_001378584.1:c.2347C>G
NM_001378585.1:c.2422C>G
NM_001378586.1:c.2422C>G
NM_002161.6:c.2422C>GMANE SELECT
NM_013417.2:c.2422C>G
NM_013417.4:c.2422C>G
NP_001361228.1:p.Arg783Gly
NP_001361229.1:p.Arg783Gly
NP_001361230.1:p.Arg780Gly
NP_001365498.1:p.Arg829Gly
NP_001365500.1:p.Arg815Gly
NP_001365501.1:p.Arg808Gly
NP_001365502.1:p.Arg808Gly
NP_001365503.1:p.Arg808Gly
NP_001365504.1:p.Arg808Gly
NP_001365505.1:p.Arg808Gly
NP_001365506.1:p.Arg808Gly
NP_001365507.1:p.Arg808Gly
NP_001365508.1:p.Arg808Gly
NP_001365509.1:p.Arg808Gly
NP_001365511.1:p.Arg776Gly
NP_001365512.1:p.Arg767Gly
NP_001365513.1:p.Arg783Gly
NP_001365514.1:p.Arg808Gly
NP_001365515.1:p.Arg808Gly
NP_002152.2:p.Arg808Gly
NP_038203.2:p.Arg808Gly
NC_000009.11:g.95013002G>C
NM_002161.6:c.2422C>G
NR_073446.2:n.2359C>G

Protein change:

R767G

Molecular consequence:

NM_001374299.1:c.2347C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374300.1:c.2347C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374301.1:c.2338C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378569.1:c.2485C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378571.1:c.2443C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378572.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378573.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378574.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378575.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378576.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378577.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378578.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378579.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378580.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378582.1:c.2326C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378583.1:c.2299C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378584.1:c.2347C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378585.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001378586.1:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002161.6:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_013417.4:c.2422C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_073446.2:n.2359C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Growth retardation, intellectual developmental disorder, hypotonia, and hepatopathy (GRIDHH)
Synonyms:: GROWTH RETARDATION, IMPAIRED INTELLECTUAL DEVELOPMENT, HYPOTONIA, AND HEPATOPATHY
Identifiers:: MONDO: MONDO:0014911; MedGen: C4310720; OMIM: 617093

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004047237	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004047237

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047237.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The missense variant in c.2422C>G (p.R808G) in IARS1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.R808G variant is observed in 9/29,438 (0.0306%) alleles from individuals of South Asian background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The amino acid Arg at position 808 is changed to a Gly changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Uncertain Significance (VUS).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 19, 2024

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