Is PROKR2 p.Arg80= (c.240C>T) pathogenic?

PROKR2 p.Arg80= (c.240C>T) is classified Likely benign in PROKR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-23). Absent from gnomAD v4.1.

How common is PROKR2 p.Arg80= (c.240C>T) in the general population?

PROKR2 p.Arg80= (c.240C>T) is absent from gnomAD v4.1 (gnomAD).

PROKR2 p.Arg80=

c.240C>T · rs2515241096 · VCV2745972

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP -0.97, phastCons 1
Overall
CADD	9.573	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PROKR2
Protein: p.Arg80=
Coding: c.240C>T
MANE Select: NM_144773
dbSNP: rs2515241096
Type: single nucleotide variant
Location: chr20:5314130 (GRCh38)
Gene constraint: LOEUF 1.492 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.50

Full PROKR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PROKR2 p.Arg80Cys Uncertain significance ★★ ⚠ same residue
PROKR2 p.Arg80His Uncertain significance ★ ⚠ same residue
PROKR2 p.Arg80Leu Uncertain significance ★ same residue
PROKR2 p.Arg164Gln Likely pathogenic ★★ same type
PROKR2 p.Glu231Lys Likely pathogenic ★★ ⚠ same type
PROKR2 p.Tyr316Ter Likely pathogenic ★★ same type
PROKR2 p.Ala103Val Uncertain significance ★★ ⚠ same type
PROKR2 p.Ala129Thr 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/prokr2-p-arg80 (accessed [today's date]).

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