Is RELA p.Pro407fs (c.1220del) pathogenic?

RELA p.Pro407fs (c.1220del) is classified Pathogenic in RELA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-03). No gnomAD frequency available for this variant.

How common is RELA p.Pro407fs (c.1220del) in the general population?

RELA p.Pro407fs (c.1220del) is no gnomAD frequency available for this variant (gnomAD).

RELA p.Pro407fs

c.1220del · rs2496826579 · VCV2826136

Pathogenic Single submitter

Classification

Pathogenic

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	escapes	premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.73	GERP -1.4
Region caveats
Repeat context	tandem	G-rich low complexity, segmental duplication · ambiguous alignment · reads may not map uniquely · confidence, not pathogenicity

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: RELA
Protein: p.Pro407fs
Coding: c.1220del
MANE Select: NM_021975
dbSNP: rs2496826579
Type: Deletion
Location: chr11:65654814 (GRCh38)
Gene constraint: LOEUF 0.4 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 73.52 · 88 PDB
Residue 407: a UniProt-annotated variant site (found in a patient diagnosed with autoimmune lymphoproliferative syndrome; uncertain significance)

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

Similar variants

RELA p.Gln389fs Pathogenic/Likely pathogenic ★★ same type
RELA p.Ala11fs Pathogenic ★ same type
RELA p.Ala345fs Likely pathogenic ★ same type
RELA p.Gly432fs Pathogenic ★ same type
RELA p.Ile183_Phe184insTer Pathogenic ★ same type
RELA p.Leu7fs Pathogenic ★ same type
RELA p.Met270fs Pathogenic ★ same type
RELA p.Pro10fs Likely pathogenic ★ 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/rela-p-pro407fs (accessed [today's date]).

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