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

Clinical significance:Uncertain significance (Last evaluated: Oct 10, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000984870.1

Allele description [Variation Report for NM_003331.5(TYK2):c.648G>A (p.Pro216=)]

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

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.648G>A (p.Pro216=)
HGVS:
  • NC_000019.10:g.10365880C>T
  • NG_007872.1:g.19693G>A
  • NM_003331.5:c.648G>AMANE SELECT
  • NP_003322.3:p.Pro216=
  • LRG_121t1:c.648G>A
  • LRG_121:g.19693G>A
  • NC_000019.9:g.10476556C>T
  • NM_003331.4:c.648G>A
Links:
dbSNP: rs142642403
NCBI 1000 Genomes Browser:
rs142642403
Molecular consequence:
  • NM_003331.5:c.648G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Immunodeficiency
Synonyms:
Immune deficiency; Decreased immune function
Identifiers:
MONDO: MONDO:0021094; MedGen: C0021051; OMIM: PS300755; Human Phenotype Ontology: HP:0002721
Name:
Recurrent skin infections
Synonyms:
Cutaneous infections; Skin infections
Identifiers:
MedGen: C1853193; Human Phenotype Ontology: HP:0001581

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001073395Diagnostics Services, CSIR - Centre for Cellular and Molecular Biologycriteria provided, single submitter
Uncertain significance
(Oct 10, 2019)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Diagnostics Services, CSIR - Centre for Cellular and Molecular Biology, SCV001073395.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)

Description

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 heterozygous state. The variant is also not present in our in-house exome database. This variant was also not reported earlier in OMIM, ClinVar and HGMD databases in any other affected individuals. In-silico splice-site aberration prediction program Human Splice Finder version 3.1 (HSF) predicted possible effect of splicing due to alteration of an exonic splicing enhancer (ESE) region by this variant. In-silico pathogenicity prediction programs like Mutation Taster2 and CADD predicted this variant as likely deleterious. However there are no functional studies performed earlier. Due to lack of enough evidence and also considering the phenotype of the patient the variant has been classified as uncertain significance as per the ACMG guidelines. The variant was observed in this patient with an another heterozygous variant (c.1694G>A) in TYK2 gene.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 19, 2021

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