VCV001367661.5 - ClinVar

NM_000204.5(CFI):c.1479C>A (p.Ser493Arg)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Uncertain significance

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000204.5(CFI):c.1479C>A (p.Ser493Arg)

Variation ID: 1367661 Accession: VCV001367661.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 4q25 4: 109742546 (GRCh38) [ NCBI UCSC ] 4: 110663702 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Mar 28, 2022	Feb 28, 2024	May 13, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_000204.5:c.1479C>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000195.3:p.Ser493Arg	missense
NM_001318057.2:c.1503C>A	NP_001304986.2:p.Ser501Arg	missense
NM_001331035.2:c.1458C>A	NP_001317964.1:p.Ser486Arg	missense
NM_001375278.1:c.1503C>A	NP_001362207.1:p.Ser501Arg	missense
NM_001375279.1:c.1479C>A	NP_001362208.1:p.Ser493Arg	missense
NM_001375280.1:c.1458C>A	NP_001362209.1:p.Ser486Arg	missense
NM_001375281.1:c.1479C>A	NP_001362210.1:p.Ser493Arg	missense
NM_001375282.1:c.1458C>A	NP_001362211.1:p.Ser486Arg	missense
NM_001375283.1:c.1422C>A	NP_001362212.1:p.Ser474Arg	missense
NM_001375284.1:c.870C>A	NP_001362213.1:p.Ser290Arg	missense
NR_164671.1:n.1226C>A		non-coding transcript variant
NR_164672.1:n.1529C>A		non-coding transcript variant
NR_164673.1:n.1503C>A		non-coding transcript variant
NC_000004.12:g.109742546G>T
NC_000004.11:g.110663702G>T
NG_007569.1:g.64440C>A
LRG_48:g.64440C>A

... more HGVS ... less HGVS

Protein change

S290R, S474R, S486R, S501R, S493R

Other names

Canonical SPDI

NC_000004.12:109742545:G:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

The Genome Aggregation Database (gnomAD) 0.00001

The Genome Aggregation Database (gnomAD), exomes 0.00001

Exome Aggregation Consortium (ExAC) 0.00002

Trans-Omics for Precision Medicine (TOPMed) 0.00002

Links

dbSNP: rs780759494 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CFI		-	-	GRCh38 GRCh37	502	515

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (1)	criteria provided, single submitter	May 13, 2023	RCV001932541.4
Age related macular degeneration 13 Atypical hemolytic-uremic syndrome with I factor anomaly Factor I deficiency	Uncertain significance (1)	criteria provided, single submitter	Nov 18, 2021	RCV002482546.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Nov 18, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Factor I deficiency Atypical hemolytic-uremic syndrome with I factor anomaly Age related macular degeneration 13 Affected status: unknown Allele origin: unknown	Fulgent Genetics, Fulgent Genetics Accession: SCV002776475.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022
Uncertain significance (May 13, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV002133819.3 First in ClinVar: Mar 28, 2022 Last updated: Feb 28, 2024	Comment: ClinVar contains an entry for this variant (Variation ID: 1367661). This variant has not been reported in the literature in individuals affected with CFI-related conditions. … (more) ClinVar contains an entry for this variant (Variation ID: 1367661). This variant has not been reported in the literature in individuals affected with CFI-related conditions. This variant is present in population databases (rs780759494, gnomAD 0.002%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 493 of the CFI protein (p.Ser493Arg). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CFI protein function. 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. (less)

Comment:

ClinVar contains an entry for this variant (Variation ID: 1367661). This variant has not been reported in the literature in individuals affected with CFI-related conditions. This variant is present in population databases (rs780759494, gnomAD 0.002%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 493 of the CFI protein (p.Ser493Arg). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CFI protein function. 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.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs780759494 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_000204.5(CFI):c.1479C>A (p.Ser493Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs780759494 ...