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NM_000511.6(FUT2):c.604C>T (p.Arg202Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
2 (Most recent: Nov 16, 2020)
Last evaluated:
Mar 18, 2016
Accession:
VCV000225366.2
Variation ID:
225366
Description:
single nucleotide variant
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NM_000511.6(FUT2):c.604C>T (p.Arg202Ter)

Allele ID
227407
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19q13.33
Genomic location
19: 48703560 (GRCh38) GRCh38 UCSC
19: 49206817 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.49206817C>T
NC_000019.10:g.48703560C>T
NM_000511.6:c.604C>T MANE Select NP_000502.4:p.Arg202Ter nonsense
... more HGVS
Protein change
R202*
Other names
-
Canonical SPDI
NC_000019.10:48703559:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00056
Exome Aggregation Consortium (ExAC) 0.00056
The Genome Aggregation Database (gnomAD) 0.00057
1000 Genomes Project 0.00080
Trans-Omics for Precision Medicine (TOPMed) 0.00063
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Links
ClinGen: CA9556294
dbSNP: rs1800028
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Mar 18, 2016 RCV000490450.1
Familial Otitis Media
confers sensitivity 1 no assertion criteria provided - RCV001291499.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
FUT2 - - GRCh38
GRCh37
5 33
LOC105447645 - - - GRCh38 - 17

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Mar 18, 2016)
criteria provided, single submitter
Method: reference population
Vitamin b12 plasma level quantitative trait locus 1
Allele origin: germline
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center
Accession: SCV000267325.1
Submitted: (Apr 14, 2016)
Evidence details
Publications
PubMed (2)
confers sensitivity
(-)
no assertion criteria provided
Method: research
Familial Otitis Media
Allele origin: unknown
University of Washington Center for Mendelian Genomics, University of Washington
Accession: SCV001480003.1
Submitted: (Nov 16, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
FUT2 Variants Confer Susceptibility to Familial Otitis Media. Santos-Cortez RLP American journal of human genetics 2018 PMID: 30401457
A second nonsecretor allele of the blood group alpha(1,2)fucosyl-transferase gene (FUT2). Henry S Vox sanguinis 1996 PMID: 8928486
Molecular basis for secretor type alpha(1,2)-fucosyltransferase gene deficiency in a Japanese population: a fusion gene generated by unequal crossover responsible for the enzyme deficiency. Koda Y American journal of human genetics 1996 PMID: 8755920

Text-mined citations for rs1800028...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Feb 20, 2021