# NM_145038.5(DRC1):c.1390C>T (p.Arg464Cys)

https://sugi.bio/variant/drc1-p-arg464cys

## Summary

**DRC1 p.Arg464Cys (c.1390C>T)** is classified **Uncertain significance** in DRC1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-01-31). AlphaMissense: likely benign (0.105); Ultra-rare (popmax 0.028%, afr); Associated with primary ciliary dyskinesia.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs377330459 · 2 submitters · 1 linked condition · AlphaMissense likely benign · ultra-rare (popmax 0.028%, afr)

## For patients & families {#patients}

This is a change in the DRC1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to primary ciliary dyskinesia.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant, Autosomal recessive, X-linked recessive |
| Age of onset (of this condition) | Neonatal |
| Prevalence | 1-5 / 10 000 (Pakistan) |
| Clinical trials | 76 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | DRC1 is a diagnostic-grade gene on 4 Genomics England panels |

**Commonly reported features of Primary ciliary dyskinesia** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Chronic otitis media — Frequent (79-30%)
- Recurrent otitis media — Frequent (79-30%)
- Nasal congestion — Frequent (79-30%)
- Chronic rhinitis — Frequent (79-30%)
- Neonatal respiratory distress — Frequent (79-30%)
- Male infertility — Frequent (79-30%)
- Recurrent sinopulmonary infections — Frequent (79-30%)
- Chronic sinusitis — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0004484/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [DRC1](https://sugi.bio/atlas/gene/DRC1/) |
| Protein change (HGVS p.) | p.Arg464Cys |
| Coding change (HGVS c.) | c.1390C>T |
| MANE Select transcript | [NM_145038](https://www.ncbi.nlm.nih.gov/nuccore/NM_145038) |
| dbSNP | [rs377330459](https://www.ncbi.nlm.nih.gov/snp/rs377330459/) |
| Variant type | single nucleotide variant |
| Location | chr2:26444942-26444942 (GRCh38) |
| ClinVar | [VCV454979](https://www.ncbi.nlm.nih.gov/clinvar/variation/454979/) |

**All HGVS expressions:** `NC_000002.11:g.26667810C>T`, `NC_000002.12:g.26444942C>T`, `NG_042824.1:g.48031C>T`, `NM_145038.2:c.1390C>T`, `NM_145038.5:c.1390C>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** (0.105)
- REVEL 0.062 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.834 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 3.47, GERP 1.58, phastCons 0.535 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 22.1**. 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 0.99** across the covering region of the MANE Select transcript (26,401,990–26,456,514), spanning 54,524 bp. Chi-square p 0.71. 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, Δ0.20 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 **0.028%** (afr) · FAF95 0.0188% · FAF99 0.0157% · 21/74,916 in the highest group · 49/1,613,748 alleles overall — ultra-rare (popmax 0.028%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.028% | 3,567 |
| East Asian | 0.00668% | 14,964 |
| Admixed American | 0.00667% | 14,994 |
| Remaining individuals (not grpmax-eligible) | 0.0064% | 15,620 |
| Finnish (not grpmax-eligible) | 0.00156% | 63,918 |
| European (non-Finnish) | 0.00136% | 73,747 |

*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}

**DRC1** population constraint: LOEUF 0.867, pLI 1.5561e-18, missense-Z 0.65957. *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):

- **primary ciliary dyskinesia 21** — Definitive (AR)

## Protein context {#protein}

Residue **464** lies in a UniProt-annotated variant site (in cild21; multiple flagellar abnormalities are present in patient sperm); a UniProt-annotated variant site (in spgf80); a UniProt-annotated variant site (in cild21).

AlphaFold model confidence (whole protein): pLDDT 75.44, 34% of residues very-high.

**1 experimental structure(s)** (PDB): [8J07](https://www.rcsb.org/structure/8J07).

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-01-31.

**Submitter consensus:** unanimous (2/2 Uncertain significance).

**Submission history:** 2 submissions (2022–2024); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-02-24 |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-01-31 |

## Associated conditions {#conditions}

[primary ciliary dyskinesia](https://sugi.bio/atlas/disease/primary-ciliary-dyskinesia/).

**Reported phenotype names (ClinVar):** Primary ciliary dyskinesia, Inborn genetic diseases, Ciliary dyskinesia.

## Similar variants {#similar}

Related DRC1 variant pages (same residue, condition, or type): [DRC1 p.Arg464His](/variant/drc1-p-arg464his), [DRC1 p.Arg464=](/variant/drc1-p-arg464), [DRC1 p.Gln118Ter](/variant/drc1-p-gln118ter), [DRC1 p.Gln337Ter](/variant/drc1-p-gln337ter), [DRC1 p.Ser642Ter](/variant/drc1-p-ser642ter), [DRC1 p.Ala250Val](/variant/drc1-p-ala250val), [DRC1 p.Ala391Val](/variant/drc1-p-ala391val), [DRC1 p.Ala416Gly](/variant/drc1-p-ala416gly).

### 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 454979). 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.*