NM_001166108.2(PALLD):c.2935C>T (p.Arg979Cys) AND Pancreatic adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 25, 2024
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:: RCV001321186.8

Allele description [Variation Report for NM_001166108.2(PALLD):c.2935C>T (p.Arg979Cys)]

NM_001166108.2(PALLD):c.2935C>T (p.Arg979Cys)

Genes:

CBR4:carbonyl reductase 4 [Gene - OMIM - HGNC]
PALLD:palladin, cytoskeletal associated protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q32.3

Genomic location:

Preferred name:

NM_001166108.2(PALLD):c.2935C>T (p.Arg979Cys)

HGVS:

NC_000004.12:g.168921618C>T
NG_013376.1:g.429553C>T
NM_001166108.2:c.2935C>TMANE SELECT
NM_001166109.2:c.1738C>T
NM_001166110.2:c.1423C>T
NM_001367567.1:c.763C>T
NM_001367568.1:c.814C>T
NM_001367569.1:c.763C>T
NM_001367570.1:c.814C>T
NM_016081.4:c.2884C>T
NP_001159580.1:p.Arg979Cys
NP_001159581.1:p.Arg580Cys
NP_001159582.1:p.Arg475Cys
NP_001354496.1:p.Arg255Cys
NP_001354497.1:p.Arg272Cys
NP_001354498.1:p.Arg255Cys
NP_001354499.1:p.Arg272Cys
NP_057165.3:p.Arg962Cys
NC_000004.11:g.169842769C>T
NM_016081.3:c.2884C>T

Protein change:

R255C

Links:

dbSNP: rs367575623

NCBI 1000 Genomes Browser:

rs367575623

Molecular consequence:

NM_001166108.2:c.2935C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001166109.2:c.1738C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001166110.2:c.1423C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001367567.1:c.763C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001367568.1:c.814C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001367569.1:c.763C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001367570.1:c.814C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016081.4:c.2884C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Pancreatic adenocarcinoma
Identifiers:: MONDO: MONDO:0006047; MedGen: C0281361; Human Phenotype Ontology: HP:0006725

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001512005	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 25, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001512005

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 25, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001512005.5

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

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 475 of the PALLD protein (p.Arg475Cys). This variant is present in population databases (rs367575623, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with PALLD-related conditions. ClinVar contains an entry for this variant (Variation ID: 1021424). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Feb 25, 2025

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