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NM_001083116.3(PRF1):c.755A>G (p.Asn252Ser) AND Familial hemophagocytic lymphohistiocytosis 2

Germline classification:
Benign (3 submissions)
Last evaluated:
Feb 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000014716.46

Allele description [Variation Report for NM_001083116.3(PRF1):c.755A>G (p.Asn252Ser)]

NM_001083116.3(PRF1):c.755A>G (p.Asn252Ser)

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.755A>G (p.Asn252Ser)
HGVS:
  • NC_000010.11:g.70598966T>C
  • NG_009615.1:g.8810A>G
  • NM_001083116.3:c.755A>GMANE SELECT
  • NM_005041.6:c.755A>G
  • NP_001076585.1:p.Asn252Ser
  • NP_005032.2:p.Asn252Ser
  • LRG_94t1:c.755A>G
  • LRG_94:g.8810A>G
  • NC_000010.10:g.72358722T>C
  • NM_001083116.1:c.755A>G
  • NM_005041.4:c.755A>G
  • P14222:p.Asn252Ser
Protein change:
N252S; ASN252SER
Links:
UniProtKB: P14222#VAR_010746; OMIM: 170280.0009; dbSNP: rs28933375
NCBI 1000 Genomes Browser:
rs28933375
Molecular consequence:
  • NM_001083116.3:c.755A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005041.6:c.755A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial hemophagocytic lymphohistiocytosis 2 (FHL2)
Identifiers:
MONDO: MONDO:0011337; MedGen: C1863727; Orphanet: 540; OMIM: 603553

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000034971OMIM
no assertion criteria provided
Uncertain significance
(Jun 1, 2005)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000644893Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Feb 1, 2024)
germlineclinical testing

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

SCV001264277Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Benign
(Apr 27, 2017)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Inherited perforin and Fas mutations in a patient with autoimmune lymphoproliferative syndrome and lymphoma.

Clementi R, Dagna L, Dianzani U, Dupré L, Dianzani I, Ponzoni M, Cometa A, Chiocchetti A, Sabbadini MG, Rugarli C, Ciceri F, Maccario R, Locatelli F, Danesino C, Ferrarini M, Bregni M.

N Engl J Med. 2004 Sep 30;351(14):1419-24.

PubMed [citation]
PMID:
15459303

Autoimmune lymphoproliferative syndrome and perforin.

Rieux-Laucat F, Le Deist F, De Saint Basile G.

N Engl J Med. 2005 Jan 20;352(3):306-7; author reply 306-7. No abstract available.

PubMed [citation]
PMID:
15659737
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000034971.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

This variant, formerly designated HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS, FAMILIAL, 2, with the 'included' title of LYMPHOMA, NON-HODGKIN, has been reclassified based on the report by Clementi et al. (2005).

In a patient with familial hemophagocytic lymphohistiocytosis (FHL2; 603553), Stepp et al. (1999) identified a 755A-G transition in the PRF1 gene, resulting in an asn252-to-ser (N252S) substitution.

In a 27-year-old man with autoimmune lymphoproliferative syndrome (601859) who later developed a T-cell-rich, histiocyte-rich, diffuse large B-cell lymphoma (605027), Clementi et al. (2004) identified a heterozygous N252S mutation in the PRF1 gene and a heterozygous mutation in the FAS gene (134637). The FAS mutation was inherited from his healthy father and was also carried by his healthy brother, whereas the PRF1 mutation was inherited from his healthy mother. Clementi et al. (2004) noted that the N252S substitution occurs within the membrane attack complex of the perforin protein, a region involved in the pore-forming activity of the molecule. However, both the patient and his mother had normal levels of perforin and normal NK cell activity. The authors suggested that the combined effect of the 2 mutant genes contributed to the development of ALPS and lymphoma in this patient. Rieux-Laucat et al. (2005) cast doubt on the pathogenicity of the N252S mutation, and the primary authors provided a rebuttal (Clementi et al., 2005).

Clementi et al. (2005) identified the N252S mutation in 1 of 660 (0.02%) control alleles, suggesting that it is a benign polymorphism.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000644893.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001264277.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

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, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

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

Last Updated: Oct 20, 2024