Is LRPPRC p.Phe184fs (c.551del) pathogenic?

LRPPRC p.Phe184fs (c.551del) is classified Pathogenic in LRPPRC (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-06). No gnomAD frequency available for this variant.

How common is LRPPRC p.Phe184fs (c.551del) in the general population?

LRPPRC p.Phe184fs (c.551del) is no gnomAD frequency available for this variant (gnomAD).

LRPPRC p.Phe184fs

c.551del · rs2103725910 · VCV1451370

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	predicted	premature termination codon in exon 4 of 38
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.6	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: LRPPRC
Protein: p.Phe184fs
Coding: c.551del
MANE Select: NM_133259
dbSNP: rs2103725910
Type: Deletion
Location: chr2:43977195 (GRCh38)
Gene constraint: LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 77.35 · 2 PDB
Residue 184: an α-helix

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

Similar variants

LRPPRC p.Phe184= Likely benign ★ same residue
LRPPRC c.1730_1735+1del Likely pathogenic ★★ same type
LRPPRC c.3710-1del Likely pathogenic ★★ same type
LRPPRC p.Ala1051fs Pathogenic/Likely pathogenic ★★ same type
LRPPRC p.Ala42fs Pathogenic/Likely pathogenic ★★ same type
LRPPRC p.Asn1246fs Pathogenic/Likely pathogenic ★★ same type
LRPPRC p.Asn454fs Pathogenic/Likely pathogenic ★★ same type
LRPPRC p.Gln1005fs 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/lrpprc-p-phe184fs (accessed [today's date]).

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