NM_031471.6(FERMT3):c.1448C>G (p.Pro483Arg) AND Leukocyte adhesion deficiency 3

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 2022
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:: RCV003045544.3

Allele description [Variation Report for NM_031471.6(FERMT3):c.1448C>G (p.Pro483Arg)]

NM_031471.6(FERMT3):c.1448C>G (p.Pro483Arg)

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.1448C>G (p.Pro483Arg)

HGVS:

NC_000011.10:g.64220572C>G
NG_016360.1:g.18893C>G
NM_001382361.1:c.1448C>G
NM_001382362.1:c.1460C>G
NM_001382363.1:c.908C>G
NM_001382364.1:c.920C>G
NM_001382448.1:c.1448C>G
NM_031471.6:c.1448C>GMANE SELECT
NM_178443.3:c.1460C>G
NP_001369290.1:p.Pro483Arg
NP_001369291.1:p.Pro487Arg
NP_001369292.1:p.Pro303Arg
NP_001369293.1:p.Pro307Arg
NP_001369377.1:p.Pro483Arg
NP_113659.3:p.Pro483Arg
NP_848537.1:p.Pro487Arg
NP_848537.1:p.Pro487Arg
LRG_180t1:c.1460C>G
LRG_180:g.18893C>G
LRG_180p1:p.Pro487Arg
NC_000011.9:g.63988044C>G
NM_178443.2:c.1460C>G

Protein change:

P303R

Molecular consequence:

NM_001382361.1:c.1448C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382362.1:c.1460C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382363.1:c.908C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382364.1:c.920C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382448.1:c.1448C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_031471.6:c.1448C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_178443.3:c.1460C>G - 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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Homo sapiens C1q and TNF related 3 (C1QTNF3), transcript variant 2, mRNA
Homo sapiens C1q and TNF related 3 (C1QTNF3), transcript variant 2, mRNA
gi|325974494|ref|NM_181435.5|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003326427	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2022)	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

SCV003326427

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2022)

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, SCV003326427.2

#	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. 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) performed at Invitae indicates that this missense variant is not expected to disrupt FERMT3 protein function. This variant has not been reported in the literature in individuals affected with FERMT3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 483 of the FERMT3 protein (p.Pro483Arg).

#	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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