NM_003680.4(YARS1):c.176T>C (p.Ile59Thr) AND Neurodevelopmental delay

Germline classification:: Likely pathogenic (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:: RCV002274090.3

Allele description [Variation Report for NM_003680.4(YARS1):c.176T>C (p.Ile59Thr)]

NM_003680.4(YARS1):c.176T>C (p.Ile59Thr)

Gene:

YARS1:tyrosyl-tRNA synthetase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p35.1

Genomic location:

Preferred name:

NM_003680.4(YARS1):c.176T>C (p.Ile59Thr)

HGVS:

NC_000001.11:g.32810939A>G
NG_008408.1:g.12094T>C
NM_003680.4:c.176T>CMANE SELECT
NP_003671.1:p.Ile59Thr
NP_003671.1:p.Ile59Thr
LRG_273t1:c.176T>C
LRG_273:g.12094T>C
LRG_273p1:p.Ile59Thr
NC_000001.10:g.33276540A>G
NM_003680.3:c.176T>C

Protein change:

I59T

Links:

dbSNP: rs774466323

NCBI 1000 Genomes Browser:

rs774466323

Molecular consequence:

NM_003680.4:c.176T>C - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

effect on protein abundance [Variation Ontology: 0052]

Condition(s)

Name:: Neurodevelopmental delay
Identifiers:: MedGen: C4022738; Human Phenotype Ontology: HP:0012758

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002559152	Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	inherited	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

SCV002559152

Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

inherited

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	inherited	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 Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille, SCV002559152.1

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

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

Last Updated: May 16, 2025

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