NM_024675.4(PALB2):c.3106_3108del (p.Val1036del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 2018
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:: RCV000480444.3

Allele description [Variation Report for NM_024675.4(PALB2):c.3106_3108del (p.Val1036del)]

NM_024675.4(PALB2):c.3106_3108del (p.Val1036del)

Gene:

PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_024675.4(PALB2):c.3106_3108del (p.Val1036del)

HGVS:

NC_000016.10:g.23621369_23621371del
NG_007406.1:g.24989_24991del
NM_024675.4:c.3106_3108delMANE SELECT
NP_078951.2:p.Val1036del
LRG_308:g.24989_24991del
NC_000016.9:g.23632690_23632692del
NM_024675.3:c.3106_3108delGTT

Protein change:

V1036del

Links:

dbSNP: rs1064795481

NCBI 1000 Genomes Browser:

rs1064795481

Molecular consequence:

NM_024675.4:c.3106_3108del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000571327	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Aug 28, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000571327

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Aug 28, 2018)

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, SCV000571327.5

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

Description

This in-frame deletion of three nucleotides in PALB2 is denoted c.3106_3108delGTT at the cDNA level and p.Val1036del (V1036del) at the protein level. The normal sequence, with the bases that are deleted in brackets, is CATT[delGTT]ATTT. This variant has not, to our knowledge, been published in the literature as a pathogenic or benign germline variant. This variant was not observed in large population cohorts (Lek 2016). This deletion of a single Valine amino acid is located in the region of interaction with RAD51, BRCA2, and POLH and in the WD4 repeat (Uniprot). In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect. Since in-frame deletions may or may not inhibit proper protein functioning, the clinical significance of this finding remains unclear at this time and we consider PALB2 Val1036del to be a variant of uncertain significance.

#	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: May 1, 2024

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