Is DLL1 p.Arg635fs (c.1903del) pathogenic?

DLL1 p.Arg635fs (c.1903del) is classified Likely pathogenic in DLL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-30). Absent from gnomAD; Associated with neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures.

How common is DLL1 p.Arg635fs (c.1903del) in the general population?

DLL1 p.Arg635fs (c.1903del) is absent from gnomAD (gnomAD).

DLL1 p.Arg635fs

Q: What condition is associated with DLL1 p.Arg635fs (c.1903del)?

DLL1 p.Arg635fs (c.1903del) is associated with neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures (ClinVar).

c.1903del · rs2483345536 · VCV2584373

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures

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 haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 9 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.9	GERP -0.26, 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: DLL1
Protein: p.Arg635fs
Coding: c.1903del
MANE Select: NM_005618
dbSNP: rs2483345536
Type: Deletion
Location: chr6:170283376 (GRCh38)
Gene constraint: LOEUF 0.236 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.24 · 1 PDB
Residue 635: a UniProt-annotated variant site (in nedbas); a UniProt-annotated variant site (in nedbas; uncertain significance)

Full DLL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DLL1 p.Arg635Cys Uncertain significance ★★ ⚠ same residue
DLL1 p.Glu673fs Pathogenic/Likely pathogenic ★★ same condition
DLL1 p.Gly282fs Pathogenic/Likely pathogenic ★★ same condition
DLL1 c.1250-8_1250-1del Likely pathogenic ★ same condition
DLL1 c.732-2del Likely pathogenic ★ same condition
DLL1 p.Ala418fs Pathogenic ★ same condition
DLL1 p.Arg61fs Pathogenic ★ same condition
DLL1 p.Cys496fs Likely pathogenic ★ 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/dll1-p-arg635fs (accessed [today's date]).

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