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NM_181523.3(PIK3R1):c.1344del (p.Lys448fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 11, 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:
RCV003770478.2

Allele description [Variation Report for NM_181523.3(PIK3R1):c.1344del (p.Lys448fs)]

NM_181523.3(PIK3R1):c.1344del (p.Lys448fs)

Gene:
PIK3R1:phosphoinositide-3-kinase regulatory subunit 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
5q13.1
Genomic location:
Preferred name:
NM_181523.3(PIK3R1):c.1344del (p.Lys448fs)
HGVS:
  • NC_000005.10:g.68293753del
  • NG_012849.2:g.82998del
  • NM_001242466.2:c.255del
  • NM_181504.4:c.534del
  • NM_181523.3:c.1344delMANE SELECT
  • NM_181524.2:c.444del
  • NP_001229395.1:p.Lys85fs
  • NP_852556.2:p.Lys178fs
  • NP_852664.1:p.Lys448fs
  • NP_852665.1:p.Lys148fs
  • LRG_453t1:c.1344del
  • LRG_453:g.82998del
  • LRG_453p1:p.Lys448fs
  • NC_000005.9:g.67589576del
  • NC_000005.9:g.67589581del
  • NM_181523.2:c.1344delA
  • NM_181523.3:c.1344delAMANE SELECT
Protein change:
K148fs
Links:
dbSNP: rs1289537429
NCBI 1000 Genomes Browser:
rs1289537429
Molecular consequence:
  • NM_001242466.2:c.255del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_181504.4:c.534del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_181523.3:c.1344del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_181524.2:c.444del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
SHORT syndrome
Synonyms:
SHORT STATURE, HYPEREXTENSIBILITY, HERNIA, OCULAR DEPRESSION, RIEGER ANOMALY, AND TEETHING DELAY; Stature, Hyperextensibility of joints or Hernia (inguinal), Ocular depression, Rieger anomaly and Teething delay; LIPODYSTROPHY, PARTIAL, WITH RIEGER ANOMALY AND SHORT STATURE
Identifiers:
MONDO: MONDO:0010026; MedGen: C0878684; Orphanet: 3163; OMIM: 269880
Name:
Agammaglobulinemia 7, autosomal recessive (AGM7)
Synonyms:
AGAMMAGLOBULINEMIA, AUTOSOMAL RECESSIVE, DUE TO PIK3R1 DEFECT
Identifiers:
MONDO: MONDO:0014083; MedGen: C3554689; OMIM: 615214
Name:
Immunodeficiency 36 (IMD36)
Synonyms:
IMMUNODEFICIENCY 36 WITH LYMPHOPROLIFERATION
Identifiers:
MONDO: MONDO:0014453; MedGen: C4014934; Orphanet: 397596; OMIM: 616005

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004589633Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 11, 2023) 		germlineclinical testing

PubMed (3)
[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

Agammaglobulinemia and absent B lineage cells in a patient lacking the p85α subunit of PI3K.

Conley ME, Dobbs AK, Quintana AM, Bosompem A, Wang YD, Coustan-Smith E, Smith AM, Perez EE, Murray PJ.

J Exp Med. 2012 Mar 12;209(3):463-70. doi: 10.1084/jem.20112533. Epub 2012 Feb 20.

PubMed [citation]
PMID:
22351933
PMCID:
PMC3302225

A human immunodeficiency caused by mutations in the PIK3R1 gene.

Deau MC, Heurtier L, Frange P, Suarez F, Bole-Feysot C, Nitschke P, Cavazzana M, Picard C, Durandy A, Fischer A, Kracker S.

J Clin Invest. 2014 Sep;124(9):3923-8. doi: 10.1172/JCI75746. Epub 2014 Aug 18. Erratum in: J Clin Invest. 2015 Apr;125(4):1764-5. doi: 10.1172/JCI81746.

PubMed [citation]
PMID:
25133428
PMCID:
PMC4153704
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004589633.1

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 998150). This variant has not been reported in the literature in individuals affected with PIK3R1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Lys448Asnfs*32) in the PIK3R1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PIK3R1 are known to be pathogenic (PMID: 22351933, 25133428).

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

Last Updated: Sep 29, 2024