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NM_001083116.3(PRF1):c.559C>T (p.Pro187Ser) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 18, 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:
RCV001844533.1

Allele description [Variation Report for NM_001083116.3(PRF1):c.559C>T (p.Pro187Ser)]

NM_001083116.3(PRF1):c.559C>T (p.Pro187Ser)

Gene:
PRF1:perforin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.1
Genomic location:
Preferred name:
NM_001083116.3(PRF1):c.559C>T (p.Pro187Ser)
HGVS:
  • NC_000010.11:g.70599162G>A
  • NG_009615.1:g.8614C>T
  • NM_001083116.3:c.559C>TMANE SELECT
  • NM_005041.6:c.559C>T
  • NP_001076585.1:p.Pro187Ser
  • NP_005032.2:p.Pro187Ser
  • LRG_94t1:c.559C>T
  • LRG_94:g.8614C>T
  • NC_000010.10:g.72358918G>A
  • NM_001083116.1:c.559C>T
Protein change:
P187S
Links:
dbSNP: rs780042742
NCBI 1000 Genomes Browser:
rs780042742
Molecular consequence:
  • NM_001083116.3:c.559C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005041.6:c.559C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002103578Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Feb 18, 2022) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Primary Immunodeficiencies in India: Molecular Diagnosis and the Role of Next-Generation Sequencing.

Arunachalam AK, Maddali M, Aboobacker FN, Korula A, George B, Mathews V, Edison ES.

J Clin Immunol. 2021 Feb;41(2):393-413. doi: 10.1007/s10875-020-00923-2. Epub 2020 Nov 23.

PubMed [citation]
PMID:
33225392
PMCID:
PMC7610931

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002103578.1

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

Description

Variant summary: PRF1 c.559C>T (p.Pro187Ser) results in a non-conservative amino acid change located in the Membrane attack complex component/perforin (MACPF) domain (IPR020864) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 248456 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.559C>T has been reported in the literature in at least one individual affected with Primary immunodeficiency diseases (Arunachalam_2020). The data does not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Sep 29, 2024