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NM_000043.6(FAS):c.115A>T (p.Lys39Ter) AND Autoimmune lymphoproliferative syndrome type 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 24, 2023
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:
RCV003517918.2

Allele description [Variation Report for NM_000043.6(FAS):c.115A>T (p.Lys39Ter)]

NM_000043.6(FAS):c.115A>T (p.Lys39Ter)

Gene:
FAS:Fas cell surface death receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000043.6(FAS):c.115A>T (p.Lys39Ter)
HGVS:
  • NC_000010.11:g.89003113A>T
  • NG_009089.2:g.17583A>T
  • NM_000043.6:c.115A>TMANE SELECT
  • NM_001320619.2:c.115A>T
  • NM_001410956.1:c.160A>T
  • NM_152871.4:c.115A>T
  • NM_152872.4:c.115A>T
  • NP_000034.1:p.Lys39Ter
  • NP_000034.1:p.Lys39Ter
  • NP_001307548.1:p.Lys39Ter
  • NP_001397885.1:p.Lys54Ter
  • NP_690610.1:p.Lys39Ter
  • NP_690611.1:p.Lys39Ter
  • LRG_134t1:c.115A>T
  • LRG_134:g.17583A>T
  • LRG_134p1:p.Lys39Ter
  • NC_000010.10:g.90762870A>T
  • NM_000043.4:c.115A>T
  • NR_028033.4:n.194A>T
  • NR_028034.4:n.194A>T
  • NR_028035.4:n.194A>T
  • NR_028036.4:n.194A>T
  • NR_135313.2:n.194A>T
  • NR_135314.2:n.281A>T
  • NR_135315.2:n.281A>T
Protein change:
K39*
Molecular consequence:
  • NR_028033.4:n.194A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028034.4:n.194A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028035.4:n.194A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028036.4:n.194A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135313.2:n.194A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135314.2:n.281A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135315.2:n.281A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000043.6:c.115A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001320619.2:c.115A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001410956.1:c.160A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152871.4:c.115A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152872.4:c.115A>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004252768Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Nov 24, 2023)
germlineclinical testing

PubMed (3)
[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

Fas preassociation required for apoptosis signaling and dominant inhibition by pathogenic mutations.

Siegel RM, Frederiksen JK, Zacharias DA, Chan FK, Johnson M, Lynch D, Tsien RY, Lenardo MJ.

Science. 2000 Jun 30;288(5475):2354-7.

PubMed [citation]
PMID:
10875918

Autoimmune lymphoproliferative syndrome due to FAS mutations outside the signal-transducing death domain: molecular mechanisms and clinical penetrance.

Hsu AP, Dowdell KC, Davis J, Niemela JE, Anderson SM, Shaw PA, Rao VK, Puck JM.

Genet Med. 2012 Jan;14(1):81-9. doi: 10.1038/gim.0b013e3182310b7d. Epub 2011 Oct 7.

PubMed [citation]
PMID:
22237435
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004252768.1

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

Description

This sequence change creates a premature translational stop signal (p.Lys39*) in the FAS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FAS are known to be pathogenic (PMID: 10875918, 22237435). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FAS-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024