Is DSCAM p.Gly1071= (c.3213C>T) pathogenic?

DSCAM p.Gly1071= (c.3213C>T) is classified Likely benign in DSCAM (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-07-03). Rare (popmax 0.469%, afr); Associated with DSCAM-related disorder.

What condition is associated with DSCAM p.Gly1071= (c.3213C>T)?

DSCAM p.Gly1071= (c.3213C>T) is associated with DSCAM-related disorder (ClinVar).

How common is DSCAM p.Gly1071= (c.3213C>T) in the general population?

DSCAM p.Gly1071= (c.3213C>T) is rare (popmax 0.469%, afr) (gnomAD).

DSCAM p.Gly1071=

c.3213C>T · rs186014927 · VCV3046759

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.469%, afr)

Conditions

DSCAM-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 0.86	GERP -2.2, phastCons 1
Overall
CADD	7.414	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.469% African / African-American · 352/75,060 alleles

Filtering AF 0.429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.413%

Overall 0.0234% 378/1,614,218 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.469%	213
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Admixed American	0.015%	6,670
European (non-Finnish)	0.000254%	393,349

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: DSCAM
Protein: p.Gly1071=
Coding: c.3213C>T
MANE Select: NM_001389
dbSNP: rs186014927
Type: single nucleotide variant
Location: chr21:40144537 (GRCh38)
Gene constraint: LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 69.98 · 1 PDB
Residue 1071: the fibronectin type-iii 2 domain

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

Disease context

DSCAM-related disorder

Similar variants

DSCAM p.Arg388Leu Uncertain significance ★ ⚠ same condition
DSCAM p.Gly1976Arg Uncertain significance ★ ⚠ same condition
DSCAM p.Lys1283Asn Uncertain significance ★ ⚠ same condition
DSCAM p.Lys391Arg Uncertain significance ★ ⚠ same condition
DSCAM p.Met1548Ile Uncertain significance ★ ⚠ same condition
DSCAM p.Thr485Ile Uncertain significance ★ ⚠ same condition
DSCAM c.5036-2A>G Uncertain significance same condition
DSCAM p.Arg1657Ter 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/dscam-p-gly1071 (accessed [today's date]).

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