Is DSCAM p.Pro1074fs (c.3219del) pathogenic?

DSCAM p.Pro1074fs (c.3219del) is classified Uncertain significance in DSCAM (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-19). Absent from gnomAD.

How common is DSCAM p.Pro1074fs (c.3219del) in the general population?

DSCAM p.Pro1074fs (c.3219del) is absent from gnomAD (gnomAD).

DSCAM p.Pro1074fs

c.3219del · rs2517198189 · VCV2808911

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 17 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DSCAM
Protein: p.Pro1074fs
Coding: c.3219del
MANE Select: NM_001389
dbSNP: rs2517198189
Type: Deletion
Location: chr21:40144531 (GRCh38)
Gene constraint: LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 69.98 · 1 PDB
Residue 1074: the fibronectin type-iii 2 domain

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

Similar variants

DSCAM p.Glu1093fs Pathogenic ★ same type
DSCAM p.Phe1206fs Pathogenic ★ same type
DSCAM p.Val618fs Pathogenic ★ same type
DSCAM c.(5035+1_5036-1 Uncertain significance ★ same type
DSCAM c.934+1del Uncertain significance ★ same type
DSCAM p.Phe909fs Uncertain significance ★ same type
DSCAM p.Pro605fs Uncertain significance ★ same type
DSCAM p.Tyr397fs Uncertain significance ★ 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-pro1074fs (accessed [today's date]).

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