# NM_000204.5(CFI):c.1354G>T (p.Ala452Ser)

https://sugi.bio/variant/cfi-p-ala452ser

## Summary

**CFI p.Ala452Ser (c.1354G>T)** is classified **Conflicting classifications of pathogenicity** in CFI (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2026-09-17). AlphaMissense: likely benign (0.3281); Very rare (popmax 0.00891%, eas); Associated with CFI-related disorder.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs750018382 · 3 submitters · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.00891%, eas)

## For patients & families {#patients}

This is a change in the CFI gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 3 submitters, and is linked to CFI-related disorder.

*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:** [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.Ala452Ser |
| Coding change (HGVS c.) | c.1354G>T |
| MANE Select transcript | [NM_000204](https://www.ncbi.nlm.nih.gov/nuccore/NM_000204) |
| dbSNP | [rs750018382](https://www.ncbi.nlm.nih.gov/snp/rs750018382/) |
| Variant type | single nucleotide variant |
| Location | chr4:109746297-109746297 (GRCh38) |
| ClinVar | [VCV2151988](https://www.ncbi.nlm.nih.gov/clinvar/variation/2151988/) |

**All HGVS expressions:** `LRG_48:g.60689G>T`, `LRG_48t1:c.1354G>T`, `NC_000004.11:g.110667453C>A`, `NC_000004.12:g.109746297C>A`, `NG_007569.1:g.60689G>T`, `NM_000204.4:c.1354G>T`, `NM_000204.5:c.1354G>T`, `NM_001318057.2:c.1378G>T`, `NM_001331035.2:c.1333G>T`, `NM_001375278.1:c.1378G>T`, `NM_001375279.1:c.1354G>T`, `NM_001375280.1:c.1333G>T`, `NM_001375281.1:c.1354G>T`, `NM_001375282.1:c.1333G>T`, `NM_001375283.1:c.1297G>T`, `NM_001375284.1:c.745G>T`, `NR_164672.1:n.1404G>T`, `NR_164673.1:n.1378G>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- AlphaMissense **likely benign** (0.3281)
- REVEL 0.802 (moderately pathogenic-leaning) — differs from AlphaMissense
- SaProt LLR -7.712 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** REVEL calls this damaging; AlphaMissense and SaProt do not
- Conservation: phyloP 5.904, GERP 1.74, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 25.2**. 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: **below the reporting threshold**. This position is scored for a different substitution (C>G, Δ0.27 donor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.00891%** (eas) · FAF95 0.00298% · FAF99 0.0018% · 4/44,904 in the highest group · 25/1,614,026 alleles overall — very rare (popmax 0.00891%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.00891% | 11,226 |
| Remaining individuals (not grpmax-eligible) | 0.0032% | 31,241 |
| European (non-Finnish) | 0.00144% | 69,413 |
| African / African-American | 0.00133% | 74,920 |
| South Asian | 0.0011% | 91,084 |

*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 **452** lies in an α-helix; 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}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-09-17.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Likely pathogenic).

**Submission history:** 3 submissions (2022–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Mayo Clinic Laboratories, Mayo Clinic | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-07-18 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-01-04 |
| Genomenon, Inc, Genomenon, Inc | Likely pathogenic | criteria provided, single submitter | curation | 2026-09-17 |

## Associated conditions {#conditions}

[CFI-related disorder](https://sugi.bio/atlas/disease/cfi-related-disorder/).

**Reported phenotype names (ClinVar):** CFI-related disorder, not provided, none provided, CFI-related condition, CFI-related disorders.

## Same-residue context {#hotspot}

Residue **452** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [CFI p.Ala452Pro](/variant/cfi-p-ala452pro). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related CFI variant pages (same residue, condition, or type): [CFI p.Ala452Thr](/variant/cfi-p-ala452thr), [CFI p.Ala452Pro](/variant/cfi-p-ala452pro), [CFI p.Ala452=](/variant/cfi-p-ala452), [CFI p.Ala452Asp](/variant/cfi-p-ala452asp), [CFI p.Arg187Ter](/variant/cfi-p-arg187ter), [CFI p.Arg474Ter](/variant/cfi-p-arg474ter), [CFI p.Trp145Ter](/variant/cfi-p-trp145ter), [CFI p.Ala153Thr](/variant/cfi-p-ala153thr).

### 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 2151988). 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.*