Is RNF13 p.Pro310fs (c.929del) pathogenic?

RNF13 p.Pro310fs (c.929del) is classified Uncertain significance in RNF13 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-01). No gnomAD frequency available for this variant; Associated with developmental and epileptic encephalopathy, 73.

What condition is associated with RNF13 p.Pro310fs (c.929del)?

RNF13 p.Pro310fs (c.929del) is associated with developmental and epileptic encephalopathy, 73 (ClinVar).

How common is RNF13 p.Pro310fs (c.929del) in the general population?

RNF13 p.Pro310fs (c.929del) is no gnomAD frequency available for this variant (gnomAD).

RNF13 p.Pro310fs

Q: How is RNF13-related severe early-onset epileptic encephalopathy inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.929del · rs2473635525 · VCV1705650

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

Conditions

developmental and epileptic encephalopathy, 73

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (10 of 10) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Region caveats
Repeat context	seg dup	· 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: RNF13
Protein: p.Pro310fs
Coding: c.929del
MANE Select: NM_183381
dbSNP: rs2473635525
Type: Deletion
Location: chr3:149960884 (GRCh38)
Gene constraint: LOEUF 0.813 · pLI 0.59 (gnomAD)
Structure: AlphaFold pLDDT 74.65 · 2 PDB
Residue 310: a UniProt-annotated variant site (found in a tumor sample; uncertain significance; abolished ability to regulate protein trafficking and localization); the 'disordered' region

Full RNF13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 73 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For RNF13-related severe early-onset epileptic encephalopathy (Orphanet):

Inheritance: Autosomal dominant
Onset: Neonatal

Similar variants

RNF13 p.Ser317fs Uncertain significance ★ same condition
RNF13 p.Val365del Conflicting classifications of pathogenicity ★ same condition
RNF13 p.Asp293_Ser294insTer Pathogenic/Likely pathogenic ★★ same condition
RNF13 p.Arg212Thr Uncertain significance ★★ ⚠ same condition
RNF13 p.His263= Benign ★★ same condition
RNF13 p.Glu301Ter Pathogenic ★ same condition
RNF13 p.Arg217Ser Uncertain significance ★ ⚠ same condition
RNF13 p.Asn88Tyr Uncertain significance ★ ⚠ 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/rnf13-p-pro310fs (accessed [today's date]).

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