# NM_000204.5(CFI):c.741T>C (p.Cys247=)

https://sugi.bio/variant/cfi-p-cys247

## Summary

**CFI p.Cys247= (c.741T>C)** is classified **Likely benign** in CFI (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-20). Very rare (popmax 0.005%, amr).

**At a glance:** Likely benign · review: Single submitter · rsID rs1308535667 · 1 submitter · very rare (popmax 0.005%, amr)

## For patients & families {#patients}

This is a change in the CFI gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter.

*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.Cys247= |
| Coding change (HGVS c.) | c.741T>C |
| MANE Select transcript | [NM_000204](https://www.ncbi.nlm.nih.gov/nuccore/NM_000204) |
| dbSNP | [rs1308535667](https://www.ncbi.nlm.nih.gov/snp/rs1308535667/) |
| Variant type | single nucleotide variant |
| Location | chr4:109760554-109760554 (GRCh38) |
| ClinVar | [VCV1648211](https://www.ncbi.nlm.nih.gov/clinvar/variation/1648211/) |

**All HGVS expressions:** `LRG_48:g.46432T>C`, `NC_000004.11:g.110681710A>G`, `NC_000004.12:g.109760554A>G`, `NG_007569.1:g.46432T>C`, `NM_000204.5:c.741T>C`, `NM_001318057.2:c.741T>C`, `NM_001331035.2:c.741T>C`, `NM_001375278.1:c.741T>C`, `NM_001375279.1:c.741T>C`, `NM_001375280.1:c.741T>C`, `NM_001375281.1:c.741T>C`, `NM_001375282.1:c.741T>C`, `NM_001375283.1:c.741T>C`, `NM_001375284.1:c.132T>C`, `NR_164671.1:n.769T>C`, `NR_164672.1:n.769T>C`, `NR_164673.1:n.769T>C`

## 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 -0.181, GERP -2.96, phastCons 0.004 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 6.187**. 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.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (A>C, Δ0.32 donor loss), 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 **0.005%** (amr) · FAF95 0.00133% · FAF99 0.000668% · 3/60,024 in the highest group · 9/1,455,344 alleles overall — very rare (popmax 0.005%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.005% | 20,008 |
| African / African-American | 0.00134% | 74,902 |
| European (non-Finnish) | 0.000426% | 234,839 |

*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 **247** lies in a disulfide bond; the ldl-receptor class a 1 domain; a β-strand.

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}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2026-01-20.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2026-01-20 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Same-residue context {#hotspot}

Residue **247** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [CFI p.Cys247Gly](/variant/cfi-p-cys247gly). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related CFI variant pages (same residue, condition, or type): [CFI p.Cys247Gly](/variant/cfi-p-cys247gly), [CFI p.Cys247Phe](/variant/cfi-p-cys247phe), [CFI p.Cys247Tyr](/variant/cfi-p-cys247tyr), [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.658+1G>A](/variant/cfi-c-658-plus-1g-a), [CFI c.905-1G>C](/variant/cfi-c-905-minus-1g-c), [CFI p.Ala258Thr](/variant/cfi-p-ala258thr).

### 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 1648211). 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.*