Is DCDC1 p.Leu206= (c.616C>T) pathogenic?

DCDC1 p.Leu206= (c.616C>T) is classified Likely benign in DCDC1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-11). Ultra-rare (popmax 0.0329%, mid); Associated with DCDC1-related disorder.

What condition is associated with DCDC1 p.Leu206= (c.616C>T)?

DCDC1 p.Leu206= (c.616C>T) is associated with DCDC1-related disorder (ClinVar).

How common is DCDC1 p.Leu206= (c.616C>T) in the general population?

DCDC1 p.Leu206= (c.616C>T) is ultra-rare (popmax 0.0329%, mid) (gnomAD).

DCDC1 p.Leu206=

c.616C>T · rs750636009 · VCV3040658

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0329%, mid)

Conditions

DCDC1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Overall
CADD	20.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0329% Middle Eastern · 2/6,082 alleles

Filtering AF 0.0128% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0101%

Overall 0.00378% 61/1,613,462 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0329%	3,041
Admixed American	0.0217%	4,611
Remaining individualsnot grpmax-eligible	0.0048%	20,820
European (non-Finnish)	0.00356%	28,090
South Asian	0.0011%	91,058

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.Leu206=
Coding: c.616C>T
MANE Select: NM_001387274
dbSNP: rs750636009
Type: single nucleotide variant
Location: chr11:31305753 (GRCh38)
Gene constraint: LOEUF 1.093 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.53
Residue 206: the doublecortin 1 domain

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-leu206 (accessed [today's date]).

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