Is PRDM5 p.Arg83fs (c.246del) pathogenic?

PRDM5 p.Arg83fs (c.246del) is classified Pathogenic in PRDM5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-24). No gnomAD frequency available for this variant.

How common is PRDM5 p.Arg83fs (c.246del) in the general population?

PRDM5 p.Arg83fs (c.246del) is no gnomAD frequency available for this variant (gnomAD).

PRDM5 p.Arg83fs

c.246del · rs2478750306 · VCV2698393

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 3 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.1, 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: PRDM5
Protein: p.Arg83fs
Coding: c.246del
MANE Select: NM_018699
dbSNP: rs2478750306
Type: Deletion
Location: chr4:120853472 (GRCh38)
Gene constraint: LOEUF 0.899 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.53 · 1 PDB
Residue 83: the set domain; an α-helix

Full PRDM5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRDM5 p.Arg83Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
PRDM5 p.Arg83His Conflicting classifications of pathogenicity ★ same residue
PRDM5 p.Arg83Ser Uncertain significance ★ ⚠ same residue
PRDM5 p.Arg83= Likely benign ★ same residue
PRDM5 p.Cys325fs Pathogenic ★★ same type
PRDM5 p.Cys378fs Pathogenic/Likely pathogenic ★★ same type
PRDM5 c.1188+14_1188+22del Likely benign ★★ same type
PRDM5 c.1728+18del Benign/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/prdm5-p-arg83fs (accessed [today's date]).

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