# NM_001099434.2(DCDC2B):c.767G>A (p.Arg256Gln)

https://sugi.bio/variant/dcdc2b-p-arg256gln

## Summary

**DCDC2B p.Arg256Gln (c.767G>A)** is classified **Likely benign** in DCDC2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-09). AlphaMissense: likely benign (0.0612); Ultra-rare (popmax 0.0164%, mid).

**At a glance:** Likely benign · review: Single submitter · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0164%, mid)

## For patients & families {#patients}

This is a change in the DCDC2B 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 | [DCDC2B](https://sugi.bio/atlas/gene/DCDC2B/) |
| Protein change (HGVS p.) | p.Arg256Gln |
| Coding change (HGVS c.) | c.767G>A |
| MANE Select transcript | [NM_001099434](https://www.ncbi.nlm.nih.gov/nuccore/NM_001099434) |
| Variant type | single nucleotide variant |
| Location | chr1:32214849-32214849 (GRCh38) |
| ClinVar | [VCV3500015](https://www.ncbi.nlm.nih.gov/clinvar/variation/3500015/) |

**All HGVS expressions:** `NC_000001.10:g.32680450G>A`, `NC_000001.11:g.32214849G>A`, `NM_001099434.2:c.767G>A`, `NR_133635.2:n.1045C>T`, `NR_133636.2:n.1186C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0612)
- REVEL 0.006 (strongly benign-leaning) — agrees with AlphaMissense
- SaProt LLR -6.674 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -1.454, GERP -3.83 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.009**. 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 1.06** across the covering region of the MANE Select transcript (32,209,094–32,215,894), spanning 6,800 bp. Chi-square p 0.21. 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 (G>T, Δ0.35 acceptor gain), 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 **0.0164%** (mid) · FAF95 0.00298% · FAF99 0.0018% · 1/6,084 in the highest group · 20/1,613,828 alleles overall — ultra-rare (popmax 0.0164%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.0164% | 6,084 |
| East Asian | 0.00891% | 11,223 |
| African / African-American | 0.00401% | 24,969 |
| South Asian | 0.0022% | 45,545 |
| European (non-Finnish) | 0.000848% | 117,989 |

*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}

**DCDC2B** population constraint: LOEUF 1.383, pLI 1.0159e-15, missense-Z -0.28449. *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 **256** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 68.12, 12% of residues very-high.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-12-09.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-12-09 |

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

## Similar variants {#similar}

Related DCDC2B variant pages (same residue, condition, or type): [DCDC2B p.Ala125Pro](/variant/dcdc2b-p-ala125pro), [DCDC2B p.Ala187Gly](/variant/dcdc2b-p-ala187gly), [DCDC2B p.Ala239Ser](/variant/dcdc2b-p-ala239ser), [DCDC2B p.Ala291Thr](/variant/dcdc2b-p-ala291thr), [DCDC2B p.Ala346Val](/variant/dcdc2b-p-ala346val), [DCDC2B p.Ala55Ser](/variant/dcdc2b-p-ala55ser), [DCDC2B p.Ala55Val](/variant/dcdc2b-p-ala55val), [DCDC2B p.Ala69Glu](/variant/dcdc2b-p-ala69glu).

### 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 3500015). 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.*