NM_005859.5(PURA):c.407_435del (p.Gln136fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 8, 2019
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:: RCV001008603.1

Allele description [Variation Report for NM_005859.5(PURA):c.407_435del (p.Gln136fs)]

NM_005859.5(PURA):c.407_435del (p.Gln136fs)

Genes:

LOC129994826:ATAC-STARR-seq lymphoblastoid active region 23260 [Gene]
PURA:purine rich element binding protein A [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q31.3

Genomic location:

Preferred name:

NM_005859.5(PURA):c.407_435del (p.Gln136fs)

HGVS:

NC_000005.10:g.140114588_140114616del
NG_041813.1:g.5466_5494del
NM_005859.5:c.407_435delMANE SELECT
NP_005850.1:p.Gln136fs
NC_000005.9:g.139494173_139494201del
NM_005859.4:c.407_435del29

Protein change:

Q136fs

Links:

dbSNP: rs1581036360

NCBI 1000 Genomes Browser:

rs1581036360

Molecular consequence:

NM_005859.5:c.407_435del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001168376	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Mar 8, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001168376

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Mar 8, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV001168376.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.407_435del29 variant in the PURA gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.407_435del29 variant causes a frameshift starting with codon Glutamine 136, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 55 of the new reading frame, denoted p.Gln136ArgfsX55. This variant causes the last 187 amino acids to be replaced with 54 incorrect amino acids and is predicted to cause loss of normal protein function through protein truncation. The c.407_435del29 variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.407_435del29 as a pathogenic variant.

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

Last Updated: Oct 14, 2023

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