# NM_000574.5(CD55):c.603T>A (p.Ser201=)

https://sugi.bio/variant/cd55-p-ser201

## Summary

**CD55 p.Ser201= (c.603T>A)** is classified **Likely benign** in CD55 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-11). Very rare (popmax 0.00223%, eas).

**At a glance:** Likely benign · review: Single submitter · 1 submitter · very rare (popmax 0.00223%, eas)

## For patients & families {#patients}

This is a change in the CD55 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 | [CD55](https://sugi.bio/atlas/gene/CD55/) |
| Protein change (HGVS p.) | p.Ser201= |
| Coding change (HGVS c.) | c.603T>A |
| MANE Select transcript | [NM_000574](https://www.ncbi.nlm.nih.gov/nuccore/NM_000574) |
| Variant type | single nucleotide variant |
| Location | chr1:207326776-207326776 (GRCh38) |
| ClinVar | [VCV4725271](https://www.ncbi.nlm.nih.gov/clinvar/variation/4725271/) |

**All HGVS expressions:** `LRG_127:g.10305T>A`, `LRG_127t1:c.603T>A`, `NC_000001.10:g.207500121T>A`, `NC_000001.11:g.207326776T>A`, `NG_007465.1:g.10305T>A`, `NM_000574.5:c.603T>A`, `NM_001114752.3:c.603T>A`, `NM_001300902.2:c.603T>A`, `NM_001300903.2:c.603T>A`, `NM_001300904.2:c.603T>A`, `NR_125349.2:n.691T>A`

## 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 -0.423, GERP 0.46 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 3.109**. 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 (T>G, Δ0.29 acceptor 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 **0.00223%** (eas) · 1/44,862 in the highest group · 1/1,461,560 alleles overall — very rare (popmax 0.00223%, eas).

*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}

**CD55** population constraint: LOEUF 1.234, pLI 1.1051e-06, missense-Z 0.32192. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **201** lies in a disulfide bond; the sushi 3 domain; a β-strand.

AlphaFold model confidence (whole protein): pLDDT 78.99, 66% of residues very-high.

**33 experimental structure(s)** (PDB): [1H03](https://www.rcsb.org/structure/1H03), [1H04](https://www.rcsb.org/structure/1H04), [1H2P](https://www.rcsb.org/structure/1H2P), [1H2Q](https://www.rcsb.org/structure/1H2Q), [1M11](https://www.rcsb.org/structure/1M11), [1NWV](https://www.rcsb.org/structure/1NWV).

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

*Describes the biological roles of CD55 (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.*

**How this variant is thought to act:** CD55's established molecular role includes virus receptor activity. p.Ser201= falls in the sushi 3 domain.


### Pathways affected {#pathways}

CD55 participates in **4 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [COPI-mediated anterograde transport](https://reactome.org/content/detail/R-HSA-6807878) | curated |
| [Class B/2 (Secretin family receptors)](https://reactome.org/content/detail/R-HSA-373080) | curated |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | curated |
| [Regulation of Complement cascade](https://reactome.org/content/detail/R-HSA-977606) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** virus receptor activity, lipid binding.

**Biological process:** positive regulation of T cell cytokine production, positive regulation of cytosolic calcium ion concentration, regulation of complement activation, regulation of lipopolysaccharide-mediated signaling pathway, negative regulation of complement activation, regulation of complement-dependent cytotoxicity.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-08-11.

**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 | 2025-08-11 |

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

## Similar variants {#similar}

Related CD55 variant pages (same residue, condition, or type): [CD55 c.286+1G>A](/variant/cd55-c-286-plus-1g-a), [CD55 c.286+2T>G](/variant/cd55-c-286-plus-2t-g), [CD55 p.Glu50Ter](/variant/cd55-p-glu50ter), [CD55 p.Trp213Ter](/variant/cd55-p-trp213ter), [CD55 c.1081+1G>C](/variant/cd55-c-1081-plus-1g-c), [CD55 p.Arg221Ser](/variant/cd55-p-arg221ser), [CD55 p.Arg357Cys](/variant/cd55-p-arg357cys), [CD55 p.Arg357His](/variant/cd55-p-arg357his).

### 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 4725271). 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.*