Is RELB p.Asp39fs (c.116del) pathogenic?

RELB p.Asp39fs (c.116del) is classified Uncertain significance in RELB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-21). No gnomAD frequency available for this variant.

How common is RELB p.Asp39fs (c.116del) in the general population?

RELB p.Asp39fs (c.116del) is no gnomAD frequency available for this variant (gnomAD).

RELB p.Asp39fs

c.116del · rs2513629216 · VCV2721672

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 2 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.3, 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: RELB
Protein: p.Asp39fs
Coding: c.116del
MANE Select: NM_006509
dbSNP: rs2513629216
Type: Deletion
Location: chr19:45002958 (GRCh38)
Gene constraint: LOEUF 0.512 · pLI 0.97 (gnomAD)
Structure: AlphaFold pLDDT 70.42 · 1 PDB
Residue 39: the 'disordered' region

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

Similar variants

RELB p.Asp39His Uncertain significance ★ ⚠ same residue
RELB p.Asp39= Likely benign ★ same residue
RELB p.Pro314fs Uncertain significance ★ same type
RELB p.Pro75_Glu77delinsGln Uncertain significance ★ same type
RELB c.106+16del Benign ★ same type
RELB c.107-9_107-7del Likely benign ★ same type
RELB c.1208-18del Likely benign ★ same type
RELB c.1277-18_1277-16del Likely 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/relb-p-asp39fs (accessed [today's date]).

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