Is RPL29 p.Pro83Ser (c.247C>T) pathogenic?

RPL29 p.Pro83Ser (c.247C>T) is classified Uncertain significance in RPL29 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-24). AlphaMissense: likely benign (0.1632); Very rare (popmax 0.000339%, nfe).

How common is RPL29 p.Pro83Ser (c.247C>T) in the general population?

RPL29 p.Pro83Ser (c.247C>T) is very rare (popmax 0.000339%, nfe) (gnomAD).

What do computational predictors say about RPL29 p.Pro83Ser (c.247C>T)?

AlphaMissense predicts likely benign (score 0.1632) — an in-silico prediction, not a clinical call.

RPL29 p.Pro83Ser

c.247C>T · rs967198475 · VCV2529209

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1632 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1632	likely benign
REVEL	0.19	benign-leaning
SaProt	LLR -9.81	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP -4.1, phastCons 1
Regional constraint	o/e 0.71	unconstrained · MANE · 1,709 bp · p 2.4e-05 · regional, not allelic
Overall
CADD	20.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,179,752 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.00025% 4/1,597,440 alleles · very rare exomes 2/1,445,208 · genomes 2/152,232 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: RPL29
Protein: p.Pro83Ser
Coding: c.247C>T
MANE Select: NM_000992
dbSNP: rs967198475
Type: single nucleotide variant
Location: chr3:51993982 (GRCh38)
Gene constraint: LOEUF 1.426 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 82.49 · 161 PDB

Full RPL29 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RPL29 p.Ala108Asp Uncertain significance ★ ⚠ same type
RPL29 p.Ala59Val Uncertain significance ★ ⚠ same type
RPL29 p.Ala67Thr Uncertain significance ★ ⚠ same type
RPL29 p.Arg107His Uncertain significance ★ ⚠ same type
RPL29 p.Arg109Cys Uncertain significance ★ ⚠ same type
RPL29 p.Arg120Gln Uncertain significance ★ ⚠ same type
RPL29 p.Arg120Pro Uncertain significance ★ ⚠ same type
RPL29 p.Arg120Trp Uncertain significance ★ ⚠ 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/rpl29-p-pro83ser (accessed [today's date]).

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