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NM_003331.5(TYK2):c.2458C>A (p.Pro820Thr) AND Immunodeficiency 35

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 15, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001922961.4

Allele description [Variation Report for NM_003331.5(TYK2):c.2458C>A (p.Pro820Thr)]

NM_003331.5(TYK2):c.2458C>A (p.Pro820Thr)

Gene:
TYK2:tyrosine kinase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_003331.5(TYK2):c.2458C>A (p.Pro820Thr)
HGVS:
  • NC_000019.10:g.10357772G>T
  • NG_007872.1:g.27801C>A
  • NM_001385197.1:c.2458C>A
  • NM_001385198.1:c.2458C>A
  • NM_001385199.1:c.2272C>A
  • NM_001385200.1:c.2458C>A
  • NM_001385201.1:c.2260C>A
  • NM_001385202.1:c.2374C>A
  • NM_001385203.1:c.2458C>A
  • NM_001385204.1:c.2458C>A
  • NM_001385205.1:c.2368C>A
  • NM_001385206.1:c.2332C>A
  • NM_001385207.1:c.2440C>A
  • NM_003331.5:c.2458C>AMANE SELECT
  • NP_001372126.1:p.Pro820Thr
  • NP_001372127.1:p.Pro820Thr
  • NP_001372128.1:p.Pro758Thr
  • NP_001372129.1:p.Pro820Thr
  • NP_001372130.1:p.Pro754Thr
  • NP_001372131.1:p.Pro792Thr
  • NP_001372132.1:p.Pro820Thr
  • NP_001372133.1:p.Pro820Thr
  • NP_001372134.1:p.Pro790Thr
  • NP_001372135.1:p.Pro778Thr
  • NP_001372136.1:p.Pro814Thr
  • NP_003322.3:p.Pro820Thr
  • LRG_121:g.27801C>A
  • NC_000019.9:g.10468448G>T
Protein change:
P754T
Links:
dbSNP: rs1220172517
NCBI 1000 Genomes Browser:
rs1220172517
Molecular consequence:
  • NM_001385197.1:c.2458C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385198.1:c.2458C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385199.1:c.2272C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385200.1:c.2458C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385201.1:c.2260C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385202.1:c.2374C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385203.1:c.2458C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385204.1:c.2458C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385205.1:c.2368C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385206.1:c.2332C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001385207.1:c.2440C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003331.5:c.2458C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Immunodeficiency 35 (IMD35)
Synonyms:
HIES WITH ATYPICAL MYCOBACTERIOSIS, AUTOSOMAL RECESSIVE; HYPER-IgE SYNDROME WITH ATYPICAL MYCOBACTERIOSIS, AUTOSOMAL RECESSIVE; TYK2 DEFICIENCY; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012682; MedGen: C1969086; OMIM: 611521

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002184945Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 15, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002184945.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces proline with threonine at codon 820 of the TYK2 protein (p.Pro820Thr). The proline residue is highly conserved and there is a small physicochemical difference between proline and threonine. This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals affected with TYK2-related conditions.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024