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NM_000431.4(MVK):c.346T>C (p.Tyr116His)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 21, 2021)
Last evaluated:
Jul 8, 2020
Accession:
VCV000097581.5
Variation ID:
97581
Description:
single nucleotide variant
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NM_000431.4(MVK):c.346T>C (p.Tyr116His)

Allele ID
103473
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q24.11
Genomic location
12: 109579921 (GRCh38) GRCh38 UCSC
12: 110017726 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.110017726T>C
NC_000012.12:g.109579921T>C
NG_007702.1:g.11227T>C
... more HGVS
Protein change
Y116H
Other names
-
Canonical SPDI
NC_000012.12:109579920:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00031
The Genome Aggregation Database (gnomAD) 0.00013
Trans-Omics for Precision Medicine (TOPMed) 0.00015
The Genome Aggregation Database (gnomAD), exomes 0.00003
Exome Aggregation Consortium (ExAC) 0.00004
Links
ClinGen: CA149812
dbSNP: rs104895382
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, single submitter Jul 8, 2020 RCV000083833.2
Pathogenic 1 criteria provided, single submitter Oct 25, 2017 RCV000220019.3
Pathogenic 1 criteria provided, single submitter Jun 20, 2020 RCV000645101.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MVK - - GRCh38
GRCh37
333 369

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 25, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000279117.8
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The Y116H missense change has been reported previously in individuals with mevalonate kinase deficiency (MKD) or hyperimmunoglobulin D syndrome (Samkari et al., 2010; Levy et … (more)
Pathogenic
(Jun 20, 2020)
criteria provided, single submitter
Method: clinical testing
Mevalonic aciduria
Hyperimmunoglobulin D with periodic fever
Porokeratosis 3, disseminated superficial actinic type
Allele origin: germline
Invitae
Accession: SCV000766843.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces tyrosine with histidine at codon 116 of the MVK protein (p.Tyr116His). The tyrosine residue is moderately conserved and there is a … (more)
Pathogenic
(Jul 08, 2020)
criteria provided, single submitter
Method: clinical testing
Hyperimmunoglobulin D with periodic fever
Allele origin: unknown
Baylor Genetics
Accession: SCV001521441.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
not provided
(-)
no assertion provided
Method: not provided
Hyperimmunoglobulin D with periodic fever
Allele origin: not provided
Unité médicale des maladies autoinflammatoires, CHRU Montpellier
Accession: SCV000115935.1
Submitted: (Jun 07, 2010)
Comment:
also involved in OMIM 25117
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
A web-based collection of genotype-phenotype associations in hereditary recurrent fevers from the Eurofever registry. Papa R Orphanet journal of rare diseases 2017 PMID: 29047407
Severe early-onset colitis revealing mevalonate kinase deficiency. Levy M Pediatrics 2013 PMID: 23979089
Significant liver disease in a patient with Y116H mutation in the MVK gene. Leyva-Vega M American journal of medical genetics. Part A 2011 PMID: 21548022
A novel missense mutation in MVK associated with MK deficiency and dyserythropoietic anemia. Samkari A Pediatrics 2010 PMID: 20194276

Text-mined citations for rs104895382...

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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 Oct 08, 2021