NM_031471.6(FERMT3):c.1507G>A (p.Val503Ile) AND Leukocyte adhesion deficiency 3

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 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:: RCV001065452.7

Allele description [Variation Report for NM_031471.6(FERMT3):c.1507G>A (p.Val503Ile)]

NM_031471.6(FERMT3):c.1507G>A (p.Val503Ile)

Gene:

FERMT3:FERM domain containing kindlin 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q13.1

Genomic location:

Preferred name:

NM_031471.6(FERMT3):c.1507G>A (p.Val503Ile)

HGVS:

NC_000011.10:g.64220631G>A
NG_016360.1:g.18952G>A
NM_001382361.1:c.1507G>A
NM_001382362.1:c.1519G>A
NM_001382363.1:c.967G>A
NM_001382364.1:c.979G>A
NM_001382448.1:c.1507G>A
NM_031471.6:c.1507G>AMANE SELECT
NM_178443.3:c.1519G>A
NP_001369290.1:p.Val503Ile
NP_001369291.1:p.Val507Ile
NP_001369292.1:p.Val323Ile
NP_001369293.1:p.Val327Ile
NP_001369377.1:p.Val503Ile
NP_113659.3:p.Val503Ile
NP_848537.1:p.Val507Ile
LRG_180:g.18952G>A
NC_000011.9:g.63988103G>A
NM_031471.5:c.1507G>A

Protein change:

V323I

Links:

dbSNP: rs769458086

NCBI 1000 Genomes Browser:

rs769458086

Molecular consequence:

NM_001382361.1:c.1507G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382362.1:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382363.1:c.967G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382364.1:c.979G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382448.1:c.1507G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_031471.6:c.1507G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_178443.3:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Leukocyte adhesion deficiency 3
Synonyms:: INTEGRIN ACTIVATION DEFICIENCY DISEASE; LEUKOCYTE ADHESION DEFICIENCY 1 VARIANT; Leukocyte adhesion deficiency, type III
Identifiers:: MONDO: MONDO:0013016; MedGen: C2748536; Orphanet: 2968; Orphanet: 99844; OMIM: 612840

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001230410	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 2019)	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

SCV001230410

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 2019)

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, SCV001230410.5

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with FERMT3-related conditions. This variant is present in population databases (rs769458086, ExAC 0.004%). This sequence change replaces valine with isoleucine at codon 503 of the FERMT3 protein (p.Val503Ile). The valine residue is moderately conserved and there is a small physicochemical difference between valine and isoleucine.

#	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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