NM_194255.4(SLC19A1):c.80A>G (p.His27Arg) AND methotrexate response - Efficacy - ClinVar

NM_194255.4(SLC19A1):c.80A>G (p.His27Arg) AND methotrexate response - Efficacy

Germline classification:: drug response (1 submission)
Last evaluated:: Mar 24, 2021
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV001788041.4

Allele description [Variation Report for NM_194255.4(SLC19A1):c.80A>G (p.His27Arg)]

NM_194255.4(SLC19A1):c.80A>G (p.His27Arg)

Gene:

SLC19A1:solute carrier family 19 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_194255.4(SLC19A1):c.80A>G (p.His27Arg)

Other names:

RFC G80A

HGVS:

NC_000021.9:g.45537880T>C
NG_028278.2:g.30264A>G
NM_001205206.4:c.80A>G
NM_001352510.2:c.-279A>G
NM_001352511.3:c.80A>G
NM_001352512.2:c.80A>G
NM_194255.4:c.80A>GMANE SELECT
NP_001192135.1:p.His27Arg
NP_001339440.1:p.His27Arg
NP_001339441.1:p.His27Arg
NP_919231.1:p.His27Arg
NC_000021.8:g.46957794T>C
NC_000021.8:g.46957794T>C
P41440:p.His27Arg

Protein change:

H27R

Links:

UniProtKB: P41440#VAR_020210; dbSNP: rs1051266

NCBI 1000 Genomes Browser:

rs1051266

Molecular consequence:

NM_001352510.2:c.-279A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001205206.4:c.80A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352511.3:c.80A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001352512.2:c.80A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_194255.4:c.80A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: methotrexate response - Efficacy
Identifiers:: MedGen: CN322736

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002031253	PharmGKB	reviewed by expert panel (Pharmacogenomics knowledge for personalized medicine)	drug response (Mar 24, 2021) Condition: methotrexate response - Efficacy Drug reported used for: Arthritis, Rheumatoid	germline	curation	PubMed (10) [See all records that cite these PMIDs] 15457444, 15677700, 17325736, 18322994, 19827168, 22450926, 26616421, 27992285, 31099054, 22992668 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002031253

PharmGKB

reviewed by expert panel

(Pharmacogenomics knowledge for personalized medicine)

drug response
(Mar 24, 2021)
Condition: methotrexate response - Efficacy
Drug reported used for: Arthritis, Rheumatoid

germline

curation

PubMed (10)
[See all records that cite these PMIDs]

Citation Link

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	curation

Citations

PubMed

Polyglutamation of methotrexate with common polymorphisms in reduced folate carrier, aminoimidazole carboxamide ribonucleotide transformylase, and thymidylate synthase are associated with methotrexate effects in rheumatoid arthritis.

Dervieux T, Furst D, Lein DO, Capps R, Smith K, Walsh M, Kremer J.

Arthritis Rheum. 2004 Sep;50(9):2766-74.

PubMed [citation]

PMID:: 15457444

Pharmacogenetic and metabolite measurements are associated with clinical status in patients with rheumatoid arthritis treated with methotrexate: results of a multicentred cross sectional observational study.

Dervieux T, Furst D, Lein DO, Capps R, Smith K, Caldwell J, Kremer J.

Ann Rheum Dis. 2005 Aug;64(8):1180-5. Epub 2005 Jan 27.

PubMed [citation]

PMID:: 15677700
PMCID:: PMC1755602

See all PubMed Citations (10)

Details of each submission

From PharmGKB, SCV002031253.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (10)

Description

PharmGKB Level of Evidence 2A: Variants in Level 2A clinical annotations are found in PharmGKB’s Tier 1 Very Important Pharmacogenes (VIPs). These variants are in known pharmacogenes, implying causation of drug phenotype is more likely. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2A clinical annotations must be supported by at least two independent publications.

#	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: Jul 23, 2024

ClinVar

Relating variation to medicine