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NM_003331.5(TYK2):c.648G>A (p.Pro216=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 6, 2020
Accession:
VCV000788263.5
Variation ID:
788263
Description:
single nucleotide variant
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NM_003331.5(TYK2):c.648G>A (p.Pro216=)

Allele ID
716121
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.2
Genomic location
19: 10365880 (GRCh38) GRCh38 UCSC
19: 10476556 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.10365880C>T
NC_000019.9:g.10476556C>T
NM_003331.5:c.648G>A MANE Select NP_003322.3:p.Pro216= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:10365879:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00031
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00055
The Genome Aggregation Database (gnomAD), exomes 0.00025
The Genome Aggregation Database (gnomAD) 0.00029
Exome Aggregation Consortium (ExAC) 0.00038
1000 Genomes Project 0.00020
Links
dbSNP: rs142642403
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 10, 2019 RCV000984870.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 6, 2020 RCV000970668.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TYK2 - - GRCh38
GRCh37
475 489

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 10, 2019)
criteria provided, single submitter
Method: clinical testing
Recurrent skin infections
Immunodeficiency
(Autosomal recessive inheritance)
Allele origin: unknown
Diagnostics Services, CSIR - Centre for Cellular and Molecular Biology
Accession: SCV001073395.1
Submitted: (Dec 13, 2019)
Evidence details
Comment:
The c.648G>A variant is present in publicly available databases like 1000 Genomes, EVS, ExAC, gnomAD and dbSNP at very low minor allele frequency (<0.0002), in … (more)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001284810.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Invitae
Accession: SCV001118261.3
Submitted: (Jan 07, 2021)
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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs142642403...

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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 Aug 19, 2021