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NM_000043.6(FAS):c.881del (p.Thr293_Leu294insTer) AND Autoimmune lymphoproliferative syndrome type 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 9, 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:
RCV003037353.3

Allele description [Variation Report for NM_000043.6(FAS):c.881del (p.Thr293_Leu294insTer)]

NM_000043.6(FAS):c.881del (p.Thr293_Leu294insTer)

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.881del (p.Thr293_Leu294insTer)
HGVS:
  • NC_000010.11:g.89014323del
  • NG_009089.2:g.28793del
  • NM_000043.6:c.881delMANE SELECT
  • NM_001320619.2:c.*204del
  • NM_001410956.1:c.926delT
  • NM_152871.4:c.818del
  • NM_152872.4:c.*193del
  • NP_000034.1:p.Leu294Terfs
  • NP_000034.1:p.Thr293_Leu294insTer
  • NP_001397885.1:p.Leu309Terfs
  • NP_690610.1:p.Thr272_Leu273insTer
  • LRG_134t1:c.881del
  • LRG_134:g.28793del
  • LRG_134p1:p.Leu294Terfs
  • NC_000010.10:g.90774079del
  • NC_000010.10:g.90774080del
  • NM_000043.4:c.881delT
  • NR_028033.4:n.788del
  • NR_028034.4:n.650del
  • NR_028035.4:n.713del
  • NR_028036.4:n.851del
  • NR_135313.2:n.768del
  • NR_135314.2:n.1047del
  • NR_135315.2:n.800del
Molecular consequence:
  • NM_001320619.2:c.*204del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_152872.4:c.*193del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001410956.1:c.926delT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_028033.4:n.788del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028034.4:n.650del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028035.4:n.713del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_028036.4:n.851del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135313.2:n.768del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135314.2:n.1047del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_135315.2:n.800del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000043.6:c.881del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001410956.1:c.926delT - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152871.4:c.818del - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003439554Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 9, 2022) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Symposium on sensorineural hearing loss in children: early detection and intervention. Delivery systems in the management of hearing impaired children.

Fellendorf GW.

Otolaryngol Clin North Am. 1975 Feb;8(1):187-218. Review.

PubMed [citation]
PMID:
1090885

Autoimmune pancreatitis in the autoimmune lymphoproliferative syndrome (ALPS): a sheep in wolves' clothing?

Langan RC, Gill F, Raiji MT, Mullinax JE, Pittaluga S, Pandalai P, Davis J, Perkins K, Avital I, Rudloff U.

Pancreas. 2013 Mar;42(2):363-6. doi: 10.1097/MPA.0b013e3182648778. No abstract available.

PubMed [citation]
PMID:
23407489
PMCID:
PMC3573327
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003439554.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Leu294*) in the FAS gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 42 amino acid(s) of the FAS protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with autoimmune lymphoproliferative syndrome (PMID: 1090885, 23407489). This variant is also known as APT1 c.1074delT. Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects FAS function (PMID: 10090885, 21490157). 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