Is DSCAM p.Arg697Gln (c.2090G>A) pathogenic?

DSCAM p.Arg697Gln (c.2090G>A) is classified Likely benign in DSCAM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-01). AlphaMissense: likely benign (0.1223); Rare (popmax 0.293%, sas).

How common is DSCAM p.Arg697Gln (c.2090G>A) in the general population?

DSCAM p.Arg697Gln (c.2090G>A) is rare (popmax 0.293%, sas) (gnomAD).

What do computational predictors say about DSCAM p.Arg697Gln (c.2090G>A)?

AlphaMissense predicts likely benign (score 0.1223) — an in-silico prediction, not a clinical call.

DSCAM p.Arg697Gln

c.2090G>A · rs201055760 · VCV2652674

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1223 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.293%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1223	likely benign
REVEL	0.104	moderately benign-leaning
SaProt	LLR -5.09	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 3.2	GERP 0.98, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 149 kb · p 1.9e-14 · regional, not allelic
Overall
CADD	24.1	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 0.293% South Asian · 267/91,078 alleles

Filtering AF 0.264% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.253%

Overall 0.0358% 578/1,614,010 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.328%	305
South Asiangrpmax	0.293%	341
Remaining individualsnot grpmax-eligible	0.0736%	1,359
Middle Eastern	0.033%	3,031
Admixed American	0.0283%	3,530
African / African-American	0.0187%	5,358
European (non-Finnish)	0.011%	9,077
Finnishnot grpmax-eligible	0.00469%	21,342
East Asian	0.00446%	22,428

Ashkenazi Jewish 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: DSCAM
Protein: p.Arg697Gln
Coding: c.2090G>A
MANE Select: NM_001389
dbSNP: rs201055760
Type: single nucleotide variant
Location: chr21:40296147 (GRCh38)
Gene constraint: LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 69.98 · 1 PDB
Residue 697: the ig-like c2-type 8 domain; an α-helix

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

Similar variants

DSCAM p.Ser682Arg Uncertain significance ★★ ⚠ same type
DSCAM c.5383+9T>A Benign ★★ same type
DSCAM p.Ala153= Benign ★★ same type
DSCAM p.Arg1798= Benign/Likely benign ★★ same type
DSCAM p.Asn1250= Benign ★★ same type
DSCAM p.Asn576= Benign/Likely benign ★★ same type
DSCAM p.Asp185= Benign/Likely benign ★★ same type
DSCAM p.Gln582= 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/dscam-p-arg697gln (accessed [today's date]).

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