NM_005359.6(SMAD4):c.72G>A (p.Met24Ile) AND Juvenile polyposis syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 16, 2023
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:: RCV003761686.2

Allele description [Variation Report for NM_005359.6(SMAD4):c.72G>A (p.Met24Ile)]

NM_005359.6(SMAD4):c.72G>A (p.Met24Ile)

Gene:

SMAD4:SMAD family member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.2

Genomic location:

Preferred name:

NM_005359.6(SMAD4):c.72G>A (p.Met24Ile)

HGVS:

NC_000018.10:g.51047118G>A
NG_013013.2:g.84079G>A
NM_001407041.1:c.72G>A
NM_001407042.1:c.72G>A
NM_001407043.1:c.72G>A
NM_005359.6:c.72G>AMANE SELECT
NP_001393970.1:p.Met24Ile
NP_001393971.1:p.Met24Ile
NP_001393972.1:p.Met24Ile
NP_005350.1:p.Met24Ile
NP_005350.1:p.Met24Ile
LRG_318t1:c.72G>A
LRG_318:g.84079G>A
LRG_318p1:p.Met24Ile
NC_000018.9:g.48573488G>A
NM_005359.5:c.72G>A
NR_176264.1:n.610G>A
NR_176265.1:n.610G>A

Protein change:

M24I

Molecular consequence:

NM_001407041.1:c.72G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407042.1:c.72G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407043.1:c.72G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005359.6:c.72G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176264.1:n.610G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176265.1:n.610G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Juvenile polyposis syndrome (JPS)
Synonyms:: Polyposis juvenile intestinal; Polyposis familial of entire gastrointestinal tract
Identifiers:: MONDO: MONDO:0017380; MedGen: C0345893; Orphanet: 2929; OMIM: 174900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004391698	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 16, 2023)	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

SCV004391698

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 16, 2023)

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, SCV004391698.1

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

Description

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. This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 24 of the SMAD4 protein (p.Met24Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SMAD4-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SMAD4 protein function.

#	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: Sep 29, 2024

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