NM_000204.5(CFI):c.1642G>C (p.Glu548Gln) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Jan 23, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000911474.21

Allele description [Variation Report for NM_000204.5(CFI):c.1642G>C (p.Glu548Gln)]

NM_000204.5(CFI):c.1642G>C (p.Glu548Gln)

Gene:

CFI:complement factor I [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q25

Genomic location:

Preferred name:

NM_000204.5(CFI):c.1642G>C (p.Glu548Gln)

HGVS:

NC_000004.12:g.109741003C>G
NG_007569.1:g.65983G>C
NM_000204.5:c.1642G>CMANE SELECT
NM_001318057.2:c.1666G>C
NM_001331035.2:c.1621G>C
NM_001375278.1:c.1558+1488G>C
NM_001375279.1:c.1534+1488G>C
NM_001375280.1:c.1513+1488G>C
NM_001375281.1:c.1534+1488G>C
NM_001375282.1:c.1513+1488G>C
NM_001375283.1:c.1585G>C
NM_001375284.1:c.1033G>C
NP_000195.2:p.Glu548Gln
NP_000195.3:p.Glu548Gln
NP_001304986.2:p.Glu556Gln
NP_001317964.1:p.Glu541Gln
NP_001362212.1:p.Glu529Gln
NP_001362213.1:p.Glu345Gln
LRG_48t1:c.1642G>C
LRG_48:g.65983G>C
NC_000004.11:g.110662159C>G
NM_000204.3:c.1642G>C
NM_000204.4:c.1642G>C
NR_164671.1:n.1389G>C
NR_164672.1:n.1692G>C
NR_164673.1:n.1666G>C
p.Glu548Gln

Protein change:

E345Q

Links:

dbSNP: rs7437875

NCBI 1000 Genomes Browser:

rs7437875

Molecular consequence:

NM_001375278.1:c.1558+1488G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001375279.1:c.1534+1488G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001375280.1:c.1513+1488G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001375281.1:c.1534+1488G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001375282.1:c.1513+1488G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000204.5:c.1642G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001318057.2:c.1666G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001331035.2:c.1621G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375283.1:c.1585G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001375284.1:c.1033G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_164671.1:n.1389G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164672.1:n.1692G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164673.1:n.1666G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001056540	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 23, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001714126	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 13, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 32510551, 35069568, 25741868
SCV001744280	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV001953383	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing
SCV001968059	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Uncertain significance	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	6	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	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

Effect of rare coding variants in the CFI gene on Factor I expression levels.

de Jong S, Volokhina EB, de Breuk A, Nilsson SC, de Jong EK, van der Kar NCAJ, Bakker B, Hoyng CB, van den Heuvel LP, Blom AM, den Hollander AI.

Hum Mol Genet. 2020 Aug 11;29(14):2313-2324. doi: 10.1093/hmg/ddaa114.

PubMed [citation]

PMID:: 32510551
PMCID:: PMC7424754

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001056540.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV001714126.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	PubMed (3)

Description

BS3_supporting

#	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		6	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001744280.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001953383.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001968059.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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