# NM_000204.5(CFI):c.1217G>A (p.Arg406His)

https://sugi.bio/variant/cfi-p-arg406his

## Summary

**CFI p.Arg406His (c.1217G>A)** is classified **Benign/Likely benign** in CFI (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-02). AlphaMissense: likely benign (0.0786); Common (popmax 9.85%, eas) — too common for a highly-penetrant pathogenic allele; Associated with atypical hemolytic-uremic syndrome with I factor anomaly.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs74817407 · 8 submitters · 2 linked conditions · AlphaMissense likely benign · common (popmax 9.85%, eas) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the CFI gene that is classified as benign/likely benign — not considered disease-causing, submitted by 8 submitters, and is linked to atypical hemolytic-uremic syndrome with I factor anomaly.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0018553/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CFI](https://sugi.bio/atlas/gene/CFI/) |
| Protein change (HGVS p.) | p.Arg406His |
| Coding change (HGVS c.) | c.1217G>A |
| MANE Select transcript | [NM_000204](https://www.ncbi.nlm.nih.gov/nuccore/NM_000204) |
| dbSNP | [rs74817407](https://www.ncbi.nlm.nih.gov/snp/rs74817407/) |
| Variant type | single nucleotide variant |
| Location | chr4:109746434-109746434 (GRCh38) |
| ClinVar | [VCV347158](https://www.ncbi.nlm.nih.gov/clinvar/variation/347158/) |

**All HGVS expressions:** `LRG_48:g.60552G>A`, `LRG_48t1:c.1217G>A`, `NC_000004.11:g.110667590C>T`, `NC_000004.12:g.109746434C>T`, `NG_007569.1:g.60552G>A`, `NM_000204.5:c.1217G>A`, `NM_001318057.2:c.1241G>A`, `NM_001331035.2:c.1196G>A`, `NM_001375278.1:c.1241G>A`, `NM_001375279.1:c.1217G>A`, `NM_001375280.1:c.1196G>A`, `NM_001375281.1:c.1217G>A`, `NM_001375282.1:c.1196G>A`, `NM_001375283.1:c.1160G>A`, `NM_001375284.1:c.608G>A`, `NR_164672.1:n.1267G>A`, `NR_164673.1:n.1241G>A`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 9.85%, eas) — too common for a highly-penetrant pathogenic allele.

- AlphaMissense **likely benign** (0.0786)
- REVEL 0.684 (pathogenic-leaning) — differs from AlphaMissense
- SaProt LLR -5.21 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** REVEL calls this damaging; AlphaMissense and SaProt do not
- Conservation: phyloP -1.898, GERP -0.991 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 8.495**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 1.00** across the covering region of the MANE Select transcript (109,740,896–109,801,971), spanning 61,075 bp. Chi-square p 0.95. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **9.85%** (eas) · FAF95 9.61% · FAF99 9.51% · 4,420/44,854 in the highest group · 12,050/1,613,494 alleles overall — common (popmax 9.85%, eas) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 9.85% | 10 |
| South Asian | 4.07% | 25 |
| Finnish (not grpmax-eligible) | 2.34% | 43 |
| Remaining individuals (not grpmax-eligible) | 1.34% | 75 |
| Middle Eastern | 0.611% | 164 |
| Admixed American | 0.355% | 281 |
| African / African-American | 0.123% | 814 |
| European (non-Finnish) | 0.106% | 945 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CFI** population constraint: LOEUF 1.076, pLI 4.9115e-15, missense-Z 0.28073. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **atypical hemolytic-uremic syndrome** — Definitive (AD)
- **C3 glomerulonephritis** — Moderate (AD)

## Protein context {#protein}

Residue **406** lies in a disulfide bond; the peptidase s1 domain.

AlphaFold model confidence (whole protein): pLDDT 84.50, 58% of residues very-high.

**2 experimental structure(s)** (PDB): [2XRC](https://www.rcsb.org/structure/2XRC), [5O32](https://www.rcsb.org/structure/5O32).

## What this gene does {#gene-function}

*Describes the biological roles of CFI (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*


### Pathways affected {#pathways}

CFI participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Regulation of Complement cascade](https://reactome.org/content/detail/R-HSA-977606) | curated |

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-02.

**Submitter consensus:** conflicting (7 Benign, 1 Likely benign).

**Submission history:** 8 submissions (2017–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Benign | criteria provided, single submitter | clinical testing | 2017-04-27 |
| Genome Diagnostics Laboratory, The Hospital for Sick Children | Benign | criteria provided, single submitter | clinical testing | 2022-09-09 |
| Genomenon, Inc, Genomenon, Inc | Benign | criteria provided, single submitter | curation | 2025-09-26 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-02 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-25 |
| Mendelics | Benign | criteria provided, single submitter | clinical testing | 2019-05-28 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Mayo Clinic Laboratories, Mayo Clinic | Benign | criteria provided, single submitter | clinical testing | 2022-09-23 |

## Associated conditions {#conditions}

[atypical hemolytic-uremic syndrome with I factor anomaly](https://sugi.bio/atlas/disease/atypical-hemolytic-uremic-syndrome-with-i-factor-anomaly/), [focal segmental glomerulosclerosis](https://sugi.bio/atlas/disease/focal-segmental-glomerulosclerosis/).

**Reported phenotype names (ClinVar):** Atypical hemolytic-uremic syndrome with I factor anomaly, not provided, Focal segmental glomerulosclerosis, CFI-related disorder, not specified, AllHighlyPenetrant, HEMOLYTIC UREMIC SYNDROME, ATYPICAL, SUSCEPTIBILITY TO, 3, AHUS, SUSCEPTIBILITY TO, 3, none provided, CFI-related disorders.

## Similar variants {#similar}

Related CFI variant pages (same residue, condition, or type): [CFI p.Arg406Cys](/variant/cfi-p-arg406cys), [CFI p.Arg406=](/variant/cfi-p-arg406), [CFI c.1429+1G>C](/variant/cfi-c-1429-plus-1g-c), [CFI c.57+1G>C](/variant/cfi-c-57-plus-1g-c), [CFI c.905-1G>C](/variant/cfi-c-905-minus-1g-c), [CFI p.Ala258Thr](/variant/cfi-p-ala258thr), [CFI p.Arg187Ter](/variant/cfi-p-arg187ter), [CFI p.Arg474Ter](/variant/cfi-p-arg474ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 347158). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*