Is DCDC1 p.Asp652Gly (c.1955A>G) pathogenic?

DCDC1 p.Asp652Gly (c.1955A>G) is classified Likely benign in DCDC1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-15). AlphaMissense: likely benign (0.1711); Rare (popmax 0.539%, nfe); Associated with DCDC1-related disorder.

What condition is associated with DCDC1 p.Asp652Gly (c.1955A>G)?

DCDC1 p.Asp652Gly (c.1955A>G) is associated with DCDC1-related disorder (ClinVar).

How common is DCDC1 p.Asp652Gly (c.1955A>G) in the general population?

DCDC1 p.Asp652Gly (c.1955A>G) is rare (popmax 0.539%, nfe) (gnomAD).

What do computational predictors say about DCDC1 p.Asp652Gly (c.1955A>G)?

AlphaMissense predicts likely benign (score 0.1711) — an in-silico prediction, not a clinical call.

DCDC1 p.Asp652Gly

c.1955A>G · rs183555899 · VCV3044015

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1711 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.539%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Conditions

DCDC1-related disorder

Computational evidence

Protein change
AlphaMissense	0.1711	likely benign
SaProt	LLR -8.64	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	Δ0.44	donor gain · deltas
Pangolin	Δ0.24	gain · loss 0.18 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 2.2	GERP 2, phastCons 0.056
Regional constraint	o/e 1.13	unconstrained · MANE · 450 kb · p 2.3e-08 · regional, not allelic
Overall
CADD	21.2	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 0.539% European (non-Finnish) · 2,133/396,042 alleles

Filtering AF 0.52% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.512%

Overall 0.416% 3,034/730,176 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.578%	173
European (non-Finnish)grpmax	0.539%	186
Ashkenazi Jewishnot grpmax-eligible	0.439%	228
Remaining individualsnot grpmax-eligible	0.395%	253
South Asian	0.274%	365
Admixed American	0.241%	415
Middle Eastern	0.138%	723
African / African-American	0.085%	1,176
East Asian	0.0247%	4,045

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp652Gly
Coding: c.1955A>G
MANE Select: NM_001387274
dbSNP: rs183555899
Type: single nucleotide variant
Location: chr11:31102205 (GRCh38)
Gene constraint: LOEUF 1.093 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.53

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

Disease context

DCDC1-related disorder

Similar variants

DCDC1 p.Cys1699Ter Likely pathogenic ★ same condition
DCDC1 c.164+3A>G Likely benign same condition
DCDC1 c.1983+10T>C Likely benign same condition
DCDC1 c.2298+8C>T Benign same condition
DCDC1 c.2716-10C>A Benign same condition
DCDC1 c.5233+7A>G Likely benign same condition
DCDC1 p.Ala684= Likely benign same condition
DCDC1 p.Ala731= Likely benign same condition

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-asp652gly (accessed [today's date]).

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