NM_001020658.2(PUM1):c.1773del (p.Ser592fs) AND Spinocerebellar ataxia 47

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 11, 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:: RCV001193938.1

Allele description [Variation Report for NM_001020658.2(PUM1):c.1773del (p.Ser592fs)]

NM_001020658.2(PUM1):c.1773del (p.Ser592fs)

Gene:

PUM1:pumilio RNA binding family member 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p35.2

Genomic location:

Preferred name:

NM_001020658.2(PUM1):c.1773del (p.Ser592fs)

HGVS:

NC_000001.11:g.30967184del
NM_001020658.2:c.1773delMANE SELECT
NM_014676.3:c.1773del
NP_001018494.1:p.Ser592fs
NP_055491.1:p.Ser592fs
NC_000001.10:g.31440031del
NM_001020658.1:c.1773del

Protein change:

S592fs

Links:

dbSNP: rs1640658015

Molecular consequence:

NM_001020658.2:c.1773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014676.3:c.1773del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Spinocerebellar ataxia 47 (NEDMSF)
Synonyms:: PADDAS SYNDROME
Identifiers:: MONDO: MONDO:0033482; MedGen: C4693672; OMIM: 620719

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001363116	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Jul 11, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001363116

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Jul 11, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363116.1

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

Description

Variant summary: PUM1 c.1773delC (p.Ser592GlnfsX32) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251234 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1773delC in individuals affected with Spinocerebellar ataxia 47 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

#	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: Jul 13, 2025

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