Is DCDC1 p.Arg963Trp (c.2887C>T) pathogenic?

DCDC1 p.Arg963Trp (c.2887C>T) is classified Likely benign in DCDC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-09). AlphaMissense: likely benign (0.0564); Rare (popmax 0.129%, nfe).

How common is DCDC1 p.Arg963Trp (c.2887C>T) in the general population?

DCDC1 p.Arg963Trp (c.2887C>T) is rare (popmax 0.129%, nfe) (gnomAD).

What do computational predictors say about DCDC1 p.Arg963Trp (c.2887C>T)?

AlphaMissense predicts likely benign (score 0.0564) — an in-silico prediction, not a clinical call.

DCDC1 p.Arg963Trp

c.2887C>T · rs150997514 · VCV3080416

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0564 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.129%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0564	likely benign
REVEL	0.201	benign-leaning
SaProt	LLR -6.52	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.6	GERP -3.5
Regional constraint	o/e 1.13	unconstrained · MANE · 450 kb · p 2.3e-08 · regional, not allelic
Overall
CADD	0.17	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.129% European (non-Finnish) · 1,520/1,177,852 alleles

Filtering AF 0.124% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.121%

Overall 0.1% 1,610/1,610,008 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.129%	775
Ashkenazi Jewishnot grpmax-eligible	0.0544%	1,840
Remaining individualsnot grpmax-eligible	0.0498%	2,009
African / African-American	0.0254%	3,939
East Asian	0.0157%	6,389
Admixed American	0.0134%	7,443
Finnishnot grpmax-eligible	0.0094%	10,640
South Asian	0.00331%	30,182

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DCDC1
Protein: p.Arg963Trp
Coding: c.2887C>T
MANE Select: NM_001387274
dbSNP: rs150997514
Type: single nucleotide variant
Location: chr11:30931781 (GRCh38)
Gene constraint: LOEUF 1.093 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.53
Residue 963: the doublecortin 2 domain

Full DCDC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCDC1 p.Gln95His Uncertain significance ★★ ⚠ same type
DCDC1 p.Thr239Met Uncertain significance ★★ ⚠ same type
DCDC1 p.Thr317Ala Uncertain significance ★★ ⚠ same type
DCDC1 c.591+13C>T Benign ★★ same type
DCDC1 p.Ala1431Thr Benign ★★ ⚠ same type
DCDC1 p.Glu200= Benign ★★ same type
DCDC1 p.Leu224= Benign ★★ same type
DCDC1 p.Lys1494Arg Benign ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dcdc1-p-arg963trp (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown