# NM_001168221.2(C2CD6):c.541C>T (p.Arg181Trp)

https://sugi.bio/variant/c2cd6-p-arg181trp

## Summary

**C2CD6 p.Arg181Trp (c.541C>T)** is classified **Uncertain significance** in C2CD6 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-15). AlphaMissense: likely benign (0.2828); Ultra-rare (popmax 0.0252%, amr).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs201483197 · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0252%, amr)

## For patients & families {#patients}

This is a change in the C2CD6 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, 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 | [C2CD6](https://sugi.bio/atlas/gene/C2CD6/) |
| Protein change (HGVS p.) | p.Arg181Trp |
| Coding change (HGVS c.) | c.541C>T |
| MANE Select transcript | [NM_001168221](https://www.ncbi.nlm.nih.gov/nuccore/NM_001168221) |
| dbSNP | [rs201483197](https://www.ncbi.nlm.nih.gov/snp/rs201483197/) |
| Variant type | single nucleotide variant |
| Location | chr2:201582193-201582193 (GRCh38) |
| ClinVar | [VCV2619025](https://www.ncbi.nlm.nih.gov/clinvar/variation/2619025/) |

**All HGVS expressions:** `NC_000002.11:g.202446916G>A`, `NC_000002.12:g.201582193G>A`, `NG_051007.1:g.41990C>T`, `NG_051007.2:g.41985C>T`, `NM_001168216.2:c.541C>T`, `NM_001168217.2:c.541C>T`, `NM_001168221.2:c.541C>T`, `NM_152525.6:c.541C>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.2828)
- REVEL 0.596 (indeterminate)
- SaProt LLR -8.775 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this tolerated; REVEL makes no call
- SpliceAI predicts **acceptor loss** (Δ 0.33) — a splice-altering prediction on an uncertain variant — a signal for review
- Conservation: phyloP 1.915, GERP -0.647, phastCons 0.951 — weakly conserved position
- CADD: **PHRED 18.18**. 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 0.96** across the covering region of the MANE Select transcript (201,536,282–201,619,130), spanning 82,848 bp. Chi-square p 0.41. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI deltas (raw): acceptor loss **0.33**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.00**. Largest is acceptor loss.
- SpliceAI deltas (masked): acceptor loss **0.33**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.00**.
- Population frequency (gnomAD v4.1): grpmax **0.0252%** (amr) · FAF95 0.0152% · FAF99 0.0122% · 14/55,480 in the highest group · 50/1,597,066 alleles overall — ultra-rare (popmax 0.0252%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.0252% | 3,963 |
| South Asian | 0.0104% | 9,638 |
| Remaining individuals (not grpmax-eligible) | 0.00647% | 15,452 |
| European (non-Finnish) | 0.00187% | 53,414 |
| African / African-American | 0.00135% | 73,814 |

*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}

**C2CD6** population constraint: LOEUF 0.908, pLI 1.1336e-26, missense-Z 3.3273. *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 **181** lies in the c2 domain.

AlphaFold model confidence (whole protein): pLDDT 39.82, 3% of residues very-high.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-08-15.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-08-15 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related C2CD6 variant pages (same residue, condition, or type): [C2CD6 p.Arg181Gln](/variant/c2cd6-p-arg181gln), [C2CD6 p.Ala1682Thr](/variant/c2cd6-p-ala1682thr), [C2CD6 p.Ala427Gly](/variant/c2cd6-p-ala427gly), [C2CD6 p.Ala54Pro](/variant/c2cd6-p-ala54pro), [C2CD6 p.Ala54Ser](/variant/c2cd6-p-ala54ser), [C2CD6 p.Ala646Ser](/variant/c2cd6-p-ala646ser), [C2CD6 p.Ala827Asp](/variant/c2cd6-p-ala827asp), [C2CD6 p.Arg1134Cys](/variant/c2cd6-p-arg1134cys).

### 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 2619025). 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.*