NM_005850.5(SF3B4):c.827del (p.Pro276fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 24, 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:: RCV000519949.1

Allele description [Variation Report for NM_005850.5(SF3B4):c.827del (p.Pro276fs)]

NM_005850.5(SF3B4):c.827del (p.Pro276fs)

Gene:

SF3B4:splicing factor 3b subunit 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q21.2

Genomic location:

Preferred name:

NM_005850.5(SF3B4):c.827del (p.Pro276fs)

HGVS:

NC_000001.11:g.149925927del
NG_032777.1:g.7331del
NM_005850.5:c.827delMANE SELECT
NP_005841.1:p.Pro276fs
NC_000001.10:g.149897819del
NM_005850.4:c.827delC

Protein change:

P276fs

Links:

dbSNP: rs797045128

NCBI 1000 Genomes Browser:

rs797045128

Molecular consequence:

NM_005850.5:c.827del - frameshift variant - [Sequence Ontology: SO:0001589]

Functional consequence:

loss_of_function_variant [Sequence Ontology: SO:0002054]

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
SCV000620490	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 24, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000620490

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 24, 2017)

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, SCV000620490.1

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

Description

The c.827delC variant in the SF3B4 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant causes a frameshift starting with codon Proline 276, changes this amino acid to a Histidine residue, and creates a premature Stop codon at position 44 of the new reading frame, denoted p.Pro276HisfsX44. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.827delC variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.827delC 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: Dec 17, 2022

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