NM_031471.6(FERMT3):c.1247T>G (p.Phe416Cys) AND Leukocyte adhesion deficiency 3

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 9, 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:: RCV002039228.4

Allele description [Variation Report for NM_031471.6(FERMT3):c.1247T>G (p.Phe416Cys)]

NM_031471.6(FERMT3):c.1247T>G (p.Phe416Cys)

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.1247T>G (p.Phe416Cys)

HGVS:

NC_000011.10:g.64220262T>G
NG_016360.1:g.18583T>G
NM_001382361.1:c.1247T>G
NM_001382362.1:c.1259T>G
NM_001382363.1:c.707T>G
NM_001382364.1:c.719T>G
NM_001382448.1:c.1247T>G
NM_031471.6:c.1247T>GMANE SELECT
NM_178443.3:c.1259T>G
NP_001369290.1:p.Phe416Cys
NP_001369291.1:p.Phe420Cys
NP_001369292.1:p.Phe236Cys
NP_001369293.1:p.Phe240Cys
NP_001369377.1:p.Phe416Cys
NP_113659.3:p.Phe416Cys
NP_848537.1:p.Phe420Cys
LRG_180:g.18583T>G
NC_000011.9:g.63987734T>G

Protein change:

F236C

Links:

dbSNP: rs772177008

NCBI 1000 Genomes Browser:

rs772177008

Molecular consequence:

NM_001382361.1:c.1247T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382362.1:c.1259T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382363.1:c.707T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382364.1:c.719T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382448.1:c.1247T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_031471.6:c.1247T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_178443.3:c.1259T>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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Ipomoea rochai (404)
GEO DataSets
Rattus norvegicus leucine-rich repeat kinase 1 (Lrrk1), mRNA
Rattus norvegicus leucine-rich repeat kinase 1 (Lrrk1), mRNA
gi|300798349|ref|NM_001191624.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002109749	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 9, 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

SCV002109749

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 9, 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, SCV002109749.3

#	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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with FERMT3-related conditions. This variant is present in population databases (rs772177008, ExAC 0.002%). This sequence change replaces phenylalanine with cysteine at codon 416 of the FERMT3 protein (p.Phe416Cys). The phenylalanine residue is moderately conserved and there is a large physicochemical difference between phenylalanine and cysteine.

#	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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