NM_000204.5(CFI):c.1322A>G (p.Lys441Arg) AND multiple conditions

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 27, 2022
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:: RCV003224266.1

Allele description [Variation Report for NM_000204.5(CFI):c.1322A>G (p.Lys441Arg)]

NM_000204.5(CFI):c.1322A>G (p.Lys441Arg)

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.1322A>G (p.Lys441Arg)

HGVS:

NC_000004.12:g.109746329T>C
NG_007569.1:g.60657A>G
NM_000204.5:c.1322A>GMANE SELECT
NM_001318057.2:c.1346A>G
NM_001331035.2:c.1301A>G
NM_001375278.1:c.1346A>G
NM_001375279.1:c.1322A>G
NM_001375280.1:c.1301A>G
NM_001375281.1:c.1322A>G
NM_001375282.1:c.1301A>G
NM_001375283.1:c.1265A>G
NM_001375284.1:c.713A>G
NP_000195.3:p.Lys441Arg
NP_001304986.2:p.Lys449Arg
NP_001317964.1:p.Lys434Arg
NP_001362207.1:p.Lys449Arg
NP_001362208.1:p.Lys441Arg
NP_001362209.1:p.Lys434Arg
NP_001362210.1:p.Lys441Arg
NP_001362211.1:p.Lys434Arg
NP_001362212.1:p.Lys422Arg
NP_001362213.1:p.Lys238Arg
LRG_48t1:c.1322A>G
LRG_48:g.60657A>G
NC_000004.11:g.110667485T>C
NM_000204.3:c.1322A>G
NM_000204.4:c.1322A>G
NR_164672.1:n.1372A>G
NR_164673.1:n.1346A>G

Protein change:

K238R

Links:

dbSNP: rs41278047

NCBI 1000 Genomes Browser:

rs41278047

Molecular consequence:

NM_000204.5:c.1322A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318057.2:c.1346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001331035.2:c.1301A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375278.1:c.1346A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375279.1:c.1322A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375280.1:c.1301A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375281.1:c.1322A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375282.1:c.1301A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375283.1:c.1265A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001375284.1:c.713A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_164672.1:n.1372A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164673.1:n.1346A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Atypical hemolytic-uremic syndrome with I factor anomaly
Synonyms:: HEMOLYTIC UREMIC SYNDROME, ATYPICAL, SUSCEPTIBILITY TO, 3; AHUS, SUSCEPTIBILITY TO, 3; Atypical hemolytic-uremic syndrome 3
Identifiers:: MONDO: MONDO:0013041; MedGen: C2752039; Orphanet: 2134; OMIM: 612923

Name:: Age related macular degeneration 13
Identifiers:: MONDO: MONDO:0014189; MedGen: C3809523; OMIM: 615439

Name:: Factor I deficiency (CFID)
Synonyms:: Complement factor I deficiency
Identifiers:: MONDO: MONDO:0012594; MedGen: C3463916; OMIM: 610984

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003919789	Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Jun 27, 2022)	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

SCV003919789

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Jun 27, 2022)

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003919789.1

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

Description

This variant is present in the Genome Aggregation Database (Highest reported MAF: 4.8% [498/10368], including 17 homozygotes; https://gnomad.broadinstitute.org/variant/4-110667485-T-C?dataset=gnomad_r2_1). It is present in ClinVar (Variation ID: 347156). Evolutionary conservation and computational predictive tools are unclear for this variant. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign.

#	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: Oct 20, 2024

ClinVar

Relating variation to medicine