NM_000204.5(CFI):c.355G>A (p.Gly119Arg) AND not provided

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Feb 18, 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:: RCV001439482.22

Allele description [Variation Report for NM_000204.5(CFI):c.355G>A (p.Gly119Arg)]

NM_000204.5(CFI):c.355G>A (p.Gly119Arg)

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.355G>A (p.Gly119Arg)

HGVS:

NC_000004.12:g.109764664C>T
NG_007569.1:g.42322G>A
NM_000204.5:c.355G>AMANE SELECT
NM_001318057.2:c.355G>A
NM_001331035.2:c.355G>A
NM_001375278.1:c.355G>A
NM_001375279.1:c.355G>A
NM_001375280.1:c.355G>A
NM_001375281.1:c.355G>A
NM_001375282.1:c.355G>A
NM_001375283.1:c.355G>A
NM_001375284.1:c.-127-2972G>A
NP_000195.2:p.Gly119Arg
NP_000195.3:p.Gly119Arg
NP_001304986.2:p.Gly119Arg
NP_001317964.1:p.Gly119Arg
NP_001362207.1:p.Gly119Arg
NP_001362208.1:p.Gly119Arg
NP_001362209.1:p.Gly119Arg
NP_001362210.1:p.Gly119Arg
NP_001362211.1:p.Gly119Arg
NP_001362212.1:p.Gly119Arg
LRG_48t1:c.355G>A
LRG_48:g.42322G>A
LRG_48p1:p.Gly119Arg
NC_000004.11:g.110685820C>T
NM_000204.3:c.355G>A
NM_000204.4:c.355G>A
NR_164671.1:n.383G>A
NR_164672.1:n.383G>A
NR_164673.1:n.383G>A
P05156:p.Gly119Arg

Protein change:

G119R; GLY119ARG

Links:

UniProtKB: P05156#VAR_063666; OMIM: 217030.0010; dbSNP: rs141853578

NCBI 1000 Genomes Browser:

rs141853578

Molecular consequence:

NM_001375284.1:c.-127-2972G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000204.5:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318057.2:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001331035.2:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375278.1:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375279.1:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375280.1:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375281.1:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375282.1:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001375283.1:c.355G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164671.1:n.383G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164672.1:n.383G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164673.1:n.383G>A - 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
SCV000521344	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Feb 18, 2022)	germline	clinical testing	Citation Link,
SCV001713310	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 22, 2020)	germline	clinical testing	PubMed (12) [See all records that cite these PMIDs] 20016463, 29500241, 25788521, 24036952, 25352734, 26691988, 26767664, 29888403, 29410599, 29392637, 23685748, 25741868 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000521344

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Feb 18, 2022)

germline

clinical testing

Citation Link,

SCV001713310

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 22, 2020)

germline

clinical testing

PubMed (12)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	2	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

Mutations in components of complement influence the outcome of Factor I-associated atypical hemolytic uremic syndrome.

Bienaime F, Dragon-Durey MA, Regnier CH, Nilsson SC, Kwan WH, Blouin J, Jablonski M, Renault N, Rameix-Welti MA, Loirat C, Sautés-Fridman C, Villoutreix BO, Blom AM, Fremeaux-Bacchi V.

Kidney Int. 2010 Feb;77(4):339-49. doi: 10.1038/ki.2009.472. Epub 2009 Dec 16.

PubMed [citation]

PMID:: 20016463

See all PubMed Citations (13)

Details of each submission

From GeneDx, SCV000521344.6

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

Description

Published functional studies demonstrate reduced expression and activity (van de Ven et al., 2013); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 20513133, 23685748, 26767664, 28637922, 28282489, 27939104, 27380463, 29398083, 29410599, 31528764, 31614353, 32510551, 32832254, 25352734, 24036952, 26691988, 29087762, 27918759, 29700787, 29888403, 29392637, 20203157, 32516404, 32195675, 33610747, 34153144, 34945728, 34169201)

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001642369.3

#	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, SCV001713310.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (12)

Description

PS3, PS4, PP3

#	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		2	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001642369	Labcorp Genetics (formerly Invitae), Labcorp	flagged submission Reason: Outlier claim with insufficient supporting evidence Notes: None (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 18, 2024)	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

SCV001642369

Labcorp Genetics (formerly Invitae), Labcorp

flagged submission

Reason: Outlier claim with insufficient supporting evidence

Notes: None

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 18, 2024)

germline

clinical testing

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

Last Updated: Nov 24, 2024

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