# NM_000204.5(CFI):c.79del (p.Asp27fs)

https://sugi.bio/variant/cfi-p-asp27fs

## Summary

**CFI p.Asp27fs (c.79del)** is classified **Pathogenic** in CFI (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-31). No gnomAD frequency available for this variant; Associated with atypical hemolytic-uremic syndrome with I factor anomaly.

**At a glance:** Pathogenic · review: Single submitter · rsID rs2545457659 · 1 submitter · 1 linked condition · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the CFI gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, 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.Asp27fs |
| Coding change (HGVS c.) | c.79del |
| MANE Select transcript | [NM_000204](https://www.ncbi.nlm.nih.gov/nuccore/NM_000204) |
| dbSNP | [rs2545457659](https://www.ncbi.nlm.nih.gov/snp/rs2545457659/) |
| Variant type | Deletion |
| Location | chr4:109766803-109766803 (GRCh38) |
| ClinVar | [VCV3061879](https://www.ncbi.nlm.nih.gov/clinvar/variation/3061879/) |

**All HGVS expressions:** `LRG_48:g.40183del`, `LRG_48t1:c.78del`, `NC_000004.11:g.110687960del`, `NC_000004.12:g.109766804del`, `NG_007569.1:g.40183del`, `NM_000204.5:c.79del`, `NM_001318057.2:c.79del`, `NM_001331035.2:c.79del`, `NM_001375278.1:c.79del`, `NM_001375279.1:c.79del`, `NM_001375280.1:c.79del`, `NM_001375281.1:c.79del`, `NM_001375282.1:c.79del`, `NM_001375283.1:c.79del`, `NM_001375284.1:c.-127-5111del`, `NR_164671.1:n.107del`, `NR_164672.1:n.107del`, `NR_164673.1:n.107del`

## Computational & population evidence {#evidence}

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

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 0.628, GERP -0.67, phastCons 0.001 — weakly conserved position
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 1.076, pLI 4.9115e-15. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 2 of 13**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*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}


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}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-03-31.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| MVZ Medizinische Genetik Mainz | Pathogenic | criteria provided, single submitter | clinical testing | 2022-03-31 |

## Associated conditions {#conditions}

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

**Reported phenotype names (ClinVar):** Atypical hemolytic-uremic syndrome with I factor anomaly, HEMOLYTIC UREMIC SYNDROME, ATYPICAL, SUSCEPTIBILITY TO, 3, AHUS, SUSCEPTIBILITY TO, 3.

## Similar variants {#similar}

Related CFI variant pages (same residue, condition, or type): [CFI p.Glu434fs](/variant/cfi-p-glu434fs), [CFI p.Met138fs](/variant/cfi-p-met138fs), [CFI p.Asp27Ala](/variant/cfi-p-asp27ala), [CFI p.Asp27Gly](/variant/cfi-p-asp27gly), [CFI p.Asp27=](/variant/cfi-p-asp27), [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).

### 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 3061879). 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.*