NM_000298.6(PKLR):c.391_393del (p.Ile131del) AND Pyruvate kinase deficiency of red cells

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 28, 2017
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:: RCV000371504.5

Allele description [Variation Report for NM_000298.6(PKLR):c.391_393del (p.Ile131del)]

NM_000298.6(PKLR):c.391_393del (p.Ile131del)

Gene:

PKLR:pyruvate kinase L/R [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q22

Genomic location:

Preferred name:

NM_000298.6(PKLR):c.391_393del (p.Ile131del)

HGVS:

NC_000001.11:g.155295552_155295554del
NG_011677.1:g.10882_10884del
NM_000298.6:c.391_393delMANE SELECT
NM_181871.4:c.298_300del
NP_000289.1:p.Ile131del
NP_870986.1:p.Ile100del
LRG_1136t1:c.391_393del
LRG_1136:g.10882_10884del
LRG_1136p1:p.Ile131del
NC_000001.10:g.155265343_155265345del
NM_000298.5:c.391_393delATC

Protein change:

I100del

Links:

dbSNP: rs886045351

NCBI 1000 Genomes Browser:

rs886045351

Molecular consequence:

NM_000298.6:c.391_393del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_181871.4:c.298_300del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Pyruvate kinase deficiency of red cells (CNSHA2)
Synonyms:: PYRUVATE KINASE DEFICIENCY OF ERYTHROCYTE; Pyruvate kinase deficiency; Pyruvate kinase deficiency of erythrocytes; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009950; MedGen: C0340968; Orphanet: 766; OMIM: 266200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000348605	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 09 May 2019)	Likely pathogenic (Apr 28, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 7919353, 7655861, 8483951 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000348605

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)

Likely pathogenic
(Apr 28, 2017)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Prenatal diagnosis of pyruvate kinase deficiency.

Baronciani L, Beutler E.

Blood. 1994 Oct 1;84(7):2354-6.

PubMed [citation]

PMID:: 7919353

Study of the molecular defects in pyruvate kinase deficient patients affected by nonspherocytic hemolytic anemia.

Baronciani L, Magalhães IQ, Mahoney DH Jr, Westwood B, Adekile AD, Lappin TR, Beutler E.

Blood Cells Mol Dis. 1995;21(1):49-55.

PubMed [citation]

PMID:: 7655861

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000348605.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The PKLR c.391_393delATC (p.Ile131del) in-frame deletion variant has been reported in three studies in which it was found in a compound heterozygous state with a second variant in three individuals with pyruvate kinase deficiency (Baronciani et al. 1993; Baronciani et al. 1994; Baronciani et al. 1995). The p.Ile131del variant was also found in a heterozygous state in an unaffected parent of one of the probands. Control data are not reported for this variant, which is not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium. PK enzyme activity in red blood cells for individuals carrying the p.Ile131del variant was shown to be from 5.9% to 24.6% of wild type activity (Baronciani et al. 1995). Based on the evidence, the p.Ile131del variant is classified as likely pathogenic for pyruvate kinase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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