Is DCC p.Asn3Ser (c.8A>G) pathogenic?

DCC p.Asn3Ser (c.8A>G) is classified Likely benign in DCC (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-08-31). AlphaMissense: likely benign (0.1558); Rare (popmax 0.508%, eas); Associated with DCC-related disorder.

What condition is associated with DCC p.Asn3Ser (c.8A>G)?

DCC p.Asn3Ser (c.8A>G) is associated with DCC-related disorder (ClinVar).

How common is DCC p.Asn3Ser (c.8A>G) in the general population?

DCC p.Asn3Ser (c.8A>G) is rare (popmax 0.508%, eas) (gnomAD).

What do computational predictors say about DCC p.Asn3Ser (c.8A>G)?

AlphaMissense predicts likely benign (score 0.1558) — an in-silico prediction, not a clinical call.

DCC p.Asn3Ser

c.8A>G · rs117282798 · VCV3059262

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1558 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.508%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

DCC-related disorder

Computational evidence

Protein change
AlphaMissense	0.1558	likely benign
REVEL	0.055	moderately benign-leaning
SaProt	LLR -4.91	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 3.8	GERP 0.4, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 1,190 kb · p 0.4 · regional, not allelic
Overall
CADD	19.46	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 0.508% East Asian · 228/44,850 alleles

Filtering AF 0.454% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.433%

Overall 0.0155% 250/1,613,694 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.508%	197
Remaining individualsnot grpmax-eligible	0.0288%	3,471
South Asian	0.00329%	30,355
European (non-Finnish)	8.48e-05%	1,179,720

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: DCC
Protein: p.Asn3Ser
Coding: c.8A>G
MANE Select: NM_005215
dbSNP: rs117282798
Type: single nucleotide variant
Location: chr18:52340795 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.60 · 9 PDB

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

Disease context

DCC-related disorder

Similar variants

DCC c.2828-1G>A Likely pathogenic ★ same condition
DCC c.3898+2T>C Likely pathogenic ★ same condition
DCC p.Arg501Ter Likely pathogenic ★ same condition
DCC p.Glu512Ter Likely pathogenic ★ same condition
DCC p.Trp508Ter Likely pathogenic ★ same condition
DCC p.Trp745Ter Likely pathogenic ★ same condition
DCC p.Pro1086Leu Uncertain significance ⚠ same condition
DCC p.Thr614Ile Uncertain significance ⚠ 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/dcc-p-asn3ser (accessed [today's date]).

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