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NM_000043.6(FAS):c.879_880del (p.Leu294fs) AND Autoimmune lymphoproliferative syndrome type 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 4, 2020
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:
RCV001382236.7

Allele description [Variation Report for NM_000043.6(FAS):c.879_880del (p.Leu294fs)]

NM_000043.6(FAS):c.879_880del (p.Leu294fs)

Gene:
FAS:Fas cell surface death receptor [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000043.6(FAS):c.879_880del (p.Leu294fs)
HGVS:
  • NC_000010.11:g.89014321_89014322del
  • NG_009089.2:g.28791_28792del
  • NM_000043.6:c.879_880delMANE SELECT
  • NM_001320619.2:c.*202_*203del
  • NM_152871.4:c.816_817del
  • NM_152872.4:c.*191_*192del
  • NP_000034.1:p.Leu294fs
  • NP_690610.1:p.Leu273fs
  • LRG_134t1:c.879_880del
  • LRG_134:g.28791_28792del
  • NC_000010.10:g.90774078_90774079del
  • NM_000043.4:c.879_880delAT
  • NR_028033.4:n.786_787del
  • NR_028034.4:n.648_649del
  • NR_028035.4:n.711_712del
  • NR_028036.4:n.849_850del
  • NR_135313.2:n.766_767del
  • NR_135314.2:n.1045_1046del
  • NR_135315.2:n.798_799del
Protein change:
L273fs
Links:
dbSNP: rs886039524
NCBI 1000 Genomes Browser:
rs886039524
Molecular consequence:
  • NM_001320619.2:c.*202_*203del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_152872.4:c.*191_*192del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000043.6:c.879_880del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_152871.4:c.816_817del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_028033.4:n.786_787del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028034.4:n.648_649del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028035.4:n.711_712del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028036.4:n.849_850del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135313.2:n.766_767del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135314.2:n.1045_1046del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135315.2:n.798_799del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Autoimmune lymphoproliferative syndrome type 1 (ALPS)
Synonyms:
Autoimmune lymphoproliferative syndrome type 1, autosomal dominant; AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME, TYPE I, AUTOSOMAL DOMINANT
Identifiers:
MONDO: MONDO:0011158; MedGen: C1328840; Orphanet: 3261; OMIM: 601859

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001580911Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Mar 4, 2020)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Autoimmune lymphoproliferative syndrome with defective Fas: genotype influences penetrance.

Jackson CE, Fischer RE, Hsu AP, Anderson SM, Choi Y, Wang J, Dale JK, Fleisher TA, Middelton LA, Sneller MC, Lenardo MJ, Straus SE, Puck JM.

Am J Hum Genet. 1999 Apr;64(4):1002-14.

PubMed [citation]
PMID:
10090885
PMCID:
PMC1377824

Advances in the applications of monoclonal antibodies in clinical oncology. 7th International meeting. 14-16 May, London, UK. Abstracts.

[No authors listed]

Eur J Cancer. 1990;26(9):1003-22. No abstract available.

PubMed [citation]
PMID:
2149015
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001580911.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the FAS protein. Other variant(s) that disrupt this region (p.L294*) have been determined to be pathogenic (PMID: 10090885, 2149015). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. This variant has been reported to affect FAS protein function (PMID: 21490157). This variant has been observed in individual(s) with autoimmune lymphoproliferative syndrome (PMID: 21490157). ClinVar contains an entry for this variant (Variation ID: 265400). This variant is not present in population databases (ExAC no frequency). This sequence change results in a premature translational stop signal in the FAS gene (p.Leu294Aspfs*2). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 42 amino acids of the FAS protein.

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

Last Updated: Sep 29, 2024