NM_031471.6(FERMT3):c.1808G>A (p.Arg603Gln) AND Leukocyte adhesion deficiency 3

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 2021
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:: RCV001037329.6

Allele description [Variation Report for NM_031471.6(FERMT3):c.1808G>A (p.Arg603Gln)]

NM_031471.6(FERMT3):c.1808G>A (p.Arg603Gln)

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.1808G>A (p.Arg603Gln)

HGVS:

NC_000011.10:g.64223185G>A
NG_016360.1:g.21506G>A
NM_001382361.1:c.1808G>A
NM_001382362.1:c.1820G>A
NM_001382363.1:c.1268G>A
NM_001382364.1:c.1280G>A
NM_001382448.1:c.1808G>A
NM_031471.6:c.1808G>AMANE SELECT
NM_178443.3:c.1820G>A
NP_001369290.1:p.Arg603Gln
NP_001369291.1:p.Arg607Gln
NP_001369292.1:p.Arg423Gln
NP_001369293.1:p.Arg427Gln
NP_001369377.1:p.Arg603Gln
NP_113659.3:p.Arg603Gln
NP_848537.1:p.Arg607Gln
LRG_180:g.21506G>A
NC_000011.9:g.63990657G>A
NM_031471.5:c.1808G>A

Protein change:

R423Q

Links:

dbSNP: rs751183978

NCBI 1000 Genomes Browser:

rs751183978

Molecular consequence:

NM_001382361.1:c.1808G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382362.1:c.1820G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382363.1:c.1268G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382364.1:c.1280G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001382448.1:c.1808G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_031471.6:c.1808G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_178443.3:c.1820G>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

Recent activity

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Acyl-CoA N-acyltransferases (NAT) superfamily protein [Arabidopsis thaliana]
Acyl-CoA N-acyltransferases (NAT) superfamily protein [Arabidopsis thaliana]
gi|15227703|ref|NP_180570.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001200739	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 28, 2021)	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

SCV001200739

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 28, 2021)

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, SCV001200739.4

#	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 with glutamine at codon 603 of the FERMT3 protein (p.Arg603Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs751183978, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with FERMT3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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: Sep 29, 2024

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