Is RBP3 p.Val102fs (c.304del) pathogenic?

RBP3 p.Val102fs (c.304del) is classified Pathogenic in RBP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-19). Absent from gnomAD.

How common is RBP3 p.Val102fs (c.304del) in the general population?

RBP3 p.Val102fs (c.304del) is absent from gnomAD (gnomAD).

RBP3 p.Val102fs

c.304del · rs2549027602 · VCV2879082

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; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.1	GERP -3.3, phastCons 0.002

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: RBP3
Protein: p.Val102fs
Coding: c.304del
MANE Select: NM_002900
dbSNP: rs2549027602
Type: Deletion
Location: chr10:47348788 (GRCh38)
Structure: AlphaFold pLDDT 63.40 · 8 PDB
Residue 102: the 'cyclin a:cdk2 binding' region; the 'interaction with birc2/c-iap1' region; the 'disordered' region

Full RBP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

E2F1 p.Ala102Thr Likely benign ★★ same residue
RBP3 c.3245+1del Likely pathogenic ★★ same type
RBP3 p.Asp427fs Pathogenic/Likely pathogenic ★★ same type
RBP3 p.Val177fs Pathogenic/Likely pathogenic ★★ same type
RBP3 p.Val411fs Pathogenic/Likely pathogenic ★★ same type
RBP3 p.Ala243fs Likely pathogenic ★ same type
RBP3 p.Arg236fs Pathogenic ★ same type
RBP3 p.Asp470fs 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/rbp3-p-val102fs (accessed [today's date]).

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