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NM_181523.3(PIK3R1):c.1945C>T (p.Arg649Trp) AND SHORT syndrome

Germline classification:
Pathogenic (8 submissions)
Last evaluated:
Jul 10, 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:
RCV000054534.48

Allele description [Variation Report for NM_181523.3(PIK3R1):c.1945C>T (p.Arg649Trp)]

NM_181523.3(PIK3R1):c.1945C>T (p.Arg649Trp)

Gene:
PIK3R1:phosphoinositide-3-kinase regulatory subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q13.1
Genomic location:
Preferred name:
NM_181523.3(PIK3R1):c.1945C>T (p.Arg649Trp)
HGVS:
  • NC_000005.10:g.68296301C>T
  • NG_012849.2:g.85546C>T
  • NM_001242466.2:c.856C>T
  • NM_181504.4:c.1135C>T
  • NM_181523.3:c.1945C>TMANE SELECT
  • NM_181524.2:c.1045C>T
  • NP_001229395.1:p.Arg286Trp
  • NP_852556.2:p.Arg379Trp
  • NP_852664.1:p.Arg649Trp
  • NP_852664.1:p.Arg649Trp
  • NP_852665.1:p.Arg349Trp
  • LRG_453t1:c.1945C>T
  • LRG_453:g.85546C>T
  • LRG_453p1:p.Arg649Trp
  • NC_000005.9:g.67592129C>T
  • NM_181523.1:c.1945C>T
  • NM_181523.2:c.1945C>T
  • P27986:p.Arg649Trp
Protein change:
R286W; ARG649TRP
Links:
UniProtKB: P27986#VAR_070223; OMIM: 171833.0004; dbSNP: rs397515453
NCBI 1000 Genomes Browser:
rs397515453
Molecular consequence:
  • NM_001242466.2:c.856C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181504.4:c.1135C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181523.3:c.1945C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181524.2:c.1045C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000083012OMIM
no assertion criteria provided
Pathogenic
(Jul 11, 2013)
germlineliterature only

PubMed (8)
[See all records that cite these PMIDs]

SCV000148015GeneReviews
no classification provided
not providedgermlineliterature only

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

SCV000255437UCLA Clinical Genomics Center, UCLA - CES
criteria provided, single submitter

(Lee et al. (JAMA. 2014))
Pathogenic
(May 13, 2014)
unknownclinical testing

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

SCV000898155Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals
no assertion criteria provided

(ACMG Guidelines, 2015)
Pathogenic
(Jul 18, 2018)
de novoclinical testing

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

SCV001976993Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 1, 2021)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV002072027Genetic Services Laboratory, University of Chicago
no assertion criteria provided
Pathogenic
(Jun 9, 2021)
germlineclinical testing

SCV0025213373billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 22, 2022)
germlineclinical testing

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

SCV005368188Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 10, 2024)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes1not providednot provided1not providedclinical testing, literature only
not providedde novoyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

SHORT syndrome: a case with high hyperopia and astigmatism.

Bonnel S, Dureau P, LeMerrer M, Dufier JL.

Ophthalmic Genet. 2000 Dec;21(4):235-8.

PubMed [citation]
PMID:
11135494

Autosomal dominant partial lipodystrophy associated with Rieger anomaly, short stature, and insulinopenic diabetes.

Aarskog D, Ose L, Pande H, Eide N.

Am J Med Genet. 1983 May;15(1):29-38.

PubMed [citation]
PMID:
6407320
See all PubMed Citations (12)

Details of each submission

From OMIM, SCV000083012.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (8)

Description

In 5 patients from 4 families with SHORT syndrome (269880), including a patient previously reported by Bonnel et al. (2000), Thauvin-Robinet et al. (2013) identified heterozygosity for a c.1945C-T transition at chr5:67,592,129 (GRCh37) in the PIK3R1 gene, resulting in an arg649-to-trp (R649W) substitution at a highly conserved residue in the cSH2 domain. In the 1 family for which parental DNA was available, the mutation was shown to be de novo. Thauvin-Robinet et al. (2013) noted that the c.1945C-T mutation occurred within the context of a CpG dinucleotide, which might explain its recurrence.

In affected members of a 3-generation Norwegian family with SHORT syndrome, originally described by Aarskog et al. (1983), and a German mother and son with SHORT syndrome, originally reported by Koenig et al. (2003), Chudasama et al. (2013) identified heterozygosity for the R649W missense mutation in the PIK3R1 gene. The mutation was not found in 340 Norwegian controls. Haplotype analysis showed that the mutations resided on different backgrounds in the 2 families, indicating that they stemmed from 2 independent mutational events. Analysis of patient fibroblasts and reconstituted Pik3r1-knockout preadipocytes demonstrated impaired interaction between p85-alpha and IRS1 (147545) and reduced AKT (see 164730)-mediated insulin signaling.

In a mother and 2 sons from an English family with SHORT syndrome, originally reported by Bankier et al. (1995) and restudied by Reardon and Temple (2008), and in an unrelated male patient, Dyment et al. (2013) identified heterozygosity for the R649W mutation in the PIK3R1 gene.

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

From GeneReviews, SCV000148015.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From UCLA Clinical Genomics Center, UCLA - CES, SCV000255437.2

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

From Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals, SCV000898155.1

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

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976993.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

PS3, PM1, PM2, PP3, PP5

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

From Genetic Services Laboratory, University of Chicago, SCV002072027.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

DNA sequence analysis of the PIK3R1 gene demonstrated a sequence change, c.1945C>T, in exon 15 that results in an amino acid change, p.Arg649Trp. This sequence change has not been described in population databases (dbSNP rs397515453). The p.Arg649Trp change affects a highly conserved amino acid residue located in a domain of the PIK3R1 protein that is known to be functional. The p.Arg649Trp substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This sequence change is a well-described missense variant that has previously been reported in multiple individuals with SHORT syndrome (PMID: 23810382, 23810379, 31829210, 29476696, 27766312, 32879144, 23980586, 32602265). Additionally, experimental studies have shown that this missense change impacts the function of the PIK3R1 protein (PMID: 27766312, 28632845, 23810379, 26974159).

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

From 3billion, SCV002521337.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.97; 3Cnet: 0.97). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000060763). The variant has been reported to co-segregate with the disease in at least 7 similarly affected relatives/individuals in at least two unrelated families (PMID: 23810382, 269880). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV005368188.1

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

Description

Criteria applied: PS3,PS4,PM2_SUP,PP3

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

Last Updated: Nov 24, 2024