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NM_003665.4(FCN3):c.349del (p.Leu117fs) AND Immunodeficiency due to ficolin3 deficiency

Germline classification:
Uncertain significance (4 submissions)
Last evaluated:
Apr 19, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000005603.9

Allele description [Variation Report for NM_003665.4(FCN3):c.349del (p.Leu117fs)]

NM_003665.4(FCN3):c.349del (p.Leu117fs)

Gene:
FCN3:ficolin 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p36.11
Genomic location:
Preferred name:
NM_003665.4(FCN3):c.349del (p.Leu117fs)
HGVS:
  • NC_000001.11:g.27373182del
  • NG_016279.1:g.6645del
  • NM_003665.4:c.349delMANE SELECT
  • NM_173452.3:c.316del
  • NP_003656.2:p.Leu117fs
  • NP_775628.1:p.Leu106fs
  • LRG_171t1:c.349del
  • LRG_171:g.6645del
  • NC_000001.10:g.27699671delG
  • NC_000001.10:g.27699673del
  • NM_003665.2:c.349del
  • NM_003665.2:c.349delC
Protein change:
L106fs
Links:
OMIM: 604973.0001; dbSNP: rs532781899
NCBI 1000 Genomes Browser:
rs532781899
Molecular consequence:
  • NM_003665.4:c.349del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_173452.3:c.316del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Immunodeficiency due to ficolin3 deficiency
Synonyms:
FICOLIN 3 DEFICIENCY; FCN3 DEFICIENCY; Immunodeficiency due to ficolin 3 deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013467; MedGen: C3151226; OMIM: 613860

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000025785OMIM
no assertion criteria provided
Pathogenic
(Jun 18, 2009)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV001135226Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Uncertain significance
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV001142296Reproductive Health Research and Development, BGI Genomics
no assertion criteria provided
Likely pathogenic
(Jan 6, 2020)
germlinecuration

SCV002786749Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Apr 19, 2022)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Immunodeficiency associated with FCN3 mutation and ficolin-3 deficiency.

Munthe-Fog L, Hummelshøj T, Honoré C, Madsen HO, Permin H, Garred P.

N Engl J Med. 2009 Jun 18;360(25):2637-44. doi: 10.1056/NEJMoa0900381.

PubMed [citation]
PMID:
19535802

Congenital H-ficolin deficiency in premature infants with severe necrotising enterocolitis.

Schlapbach LJ, Thiel S, Kessler U, Ammann RA, Aebi C, Jensenius JC.

Gut. 2011 Oct;60(10):1438-9. doi: 10.1136/gut.2010.226027. Epub 2010 Oct 22. No abstract available.

PubMed [citation]
PMID:
20971976
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000025785.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a man with immunodeficiency and recurrent infections since childhood, associated with ficolin-3 deficiency (613860), Munthe-Fog et al. (2009) identified homozygosity for a 1-bp deletion (1637delC; rs28357092) in exon 5 of the FCN3 gene, resulting in a frameshift and premature termination. Other features included brain abscesses and recurrent warts on the fingers. He had normal levels of lymphocytes, normal T-cell responses, and normal antibodies, but a selective deficient antibody response to pneumococcal polysaccharide vaccine. Laboratory studies showed impaired complement deposition when acetylated bovine serum albumin was used, indicating a defect in complement activation. The patient was born of Macedonian and Albanian parents, each of whom was unaffected and heterozygous for the variant. The allele frequency of the variant was 0.01 among a total of 1,282 patients with various immunodeficiencies; all were heterozygous for the variant except the index patient.

Schlapbach et al. (2011) reported a premature infant with necrotizing enterocolitis who was homozygous for the c.1637delC polymorphism. He had severe FCN3 deficiency, and his parents, who were heterozygous for the polymorphism, had about 50% FCN3 levels compared to controls.

Michalski et al. (2012) reported a male infant born at 35 weeks' gestation who developed infection with Streptococcus agalactiae. Laboratory studies showed complete H-ficolin deficiency as well as low MBL, undetectable MASP2, and low L-ficolin (FCN2; 601624). He had no severe infections during a 5-year follow-up, but he did have microcephaly, poor growth, and mental retardation. The patient was homozygous for the common FCN3 truncating polymorphism.

Michalski et al. (2015) reported 2 unrelated patients with ficolin-3 deficiency due to homozygosity for the c.1637delC variant. One was a 50-year-old man with nephrotic syndrome due to membranous nephropathy. The other patient was an 11-month-old boy who had pneumonia before surgery to repair a cardiac ventricular septal defect. Michalski et al. (2015) concluded that the consequences of FCN3 deficiency are not clear-cut, and suggested that it may act as a disease modifier.

Michalski et al. (2012) evaluated serum H-ficolin levels in 613 neonates, and FCN3 genotypes in 529 neonates; all were of Polish descent. Genotype analysis revealed that 96% were homozygous wildtype, 3.8% were compound heterozygous, and 0.2% (1 infant) was homozygous for the variant allele. The protein was undetectable in the homozygous infant. Preterm delivery and low birthweight were significantly associated with low serum H-ficolin, but not with heterozygosity for the c.1637delC allele, even though the variant allele influenced the protein level. There was no association between heterozygosity for the allele and perinatal infections. Michalski et al. (2012) concluded that heterozygosity for the FCN3 variant does not seem to have major clinical importance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV001135226.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Reproductive Health Research and Development, BGI Genomics, SCV001142296.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_003665.2:c.349delC in the FCN3 gene has an allele frequency of 0.028 in South Asian subpopulation in the gnomAD database. The c.349delC variant has been identified in the homozygous state in 3 individuals with Immunodeficiency (PMID: 19535802; 20971976; 22226667). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Taken together, we interprete this variant as Pathogenic/Likely pathogenic variant. ACMG/AMP criteria applied: PVS1; PM3.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002786749.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 2, 2023