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NM_003331.5(TYK2):c.3310C>G (p.Pro1104Ala)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Apr 26, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000137869.5
Variation ID:
137869
Description:
single nucleotide variant
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NM_003331.5(TYK2):c.3310C>G (p.Pro1104Ala)

Allele ID
141572
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.2
Genomic location
19: 10352442 (GRCh38) GRCh38 UCSC
19: 10463118 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.10352442G>C
NC_000019.9:g.10463118G>C
NM_003331.5:c.3310C>G MANE Select NP_003322.3:p.Pro1104Ala missense
... more HGVS
Protein change
P1104A
Other names
p.P1104A:CCC>GCC
TYK2, PRO1104ALA (rs34536443)
Canonical SPDI
NC_000019.10:10352441:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.01018 (C)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02899
Trans-Omics for Precision Medicine (TOPMed) 0.02792
The Genome Aggregation Database (gnomAD), exomes 0.02680
Exome Aggregation Consortium (ExAC) 0.02734
The Genome Aggregation Database (gnomAD) 0.02848
1000 Genomes Project 0.01018
Links
OMIM: 176941.0007
dbSNP: rs34536443
ClinGen: CA291554
UniProtKB: P29597#VAR_041874
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Apr 28, 2014 RCV000126195.2
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000528354.5
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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
466 480

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000309572.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Apr 28, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169690.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000410277.3
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)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Immunodeficiency 35
Allele origin: germline
Invitae
Accession: SCV000645761.3
Submitted: (Jan 07, 2021)
Evidence details
Pathogenic
(Apr 26, 2021)
no assertion criteria provided
Method: literature only
IMMUNODEFICIENCY 35
Allele origin: germline
OMIM
Accession: SCV001572334.1
Submitted: (Apr 26, 2021)
Evidence details
Publications
PubMed (2)

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
Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years. Kerner G American journal of human genetics 2021 PMID: 33667394
Tuberculosis and impaired IL-23-dependent IFN-γ immunity in humans homozygous for a common <i>TYK2</i> missense variant. Boisson-Dupuis S Science immunology 2018 PMID: 30578352

Text-mined citations for rs34536443...

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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 27, 2021