Is PRRC2A p.Pro1592= (c.4776A>G) pathogenic?

PRRC2A p.Pro1592= (c.4776A>G) is classified Likely benign in PRRC2A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-18). No allele count reported in gnomAD v4.1 (AN 1,610,568); Associated with PRRC2A-related disorder.

What condition is associated with PRRC2A p.Pro1592= (c.4776A>G)?

PRRC2A p.Pro1592= (c.4776A>G) is associated with PRRC2A-related disorder (ClinVar).

How common is PRRC2A p.Pro1592= (c.4776A>G) in the general population?

PRRC2A p.Pro1592= (c.4776A>G) is no allele count reported in gnomAD v4.1 (AN 1,610,568) (gnomAD).

PRRC2A p.Pro1592=

c.4776A>G · rs2533849351 · VCV3038144

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,568)

Conditions

PRRC2A-related disorder

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 0.023	GERP -0.42, phastCons 0.004
Overall
CADD	8.542	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,568). 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: PRRC2A
Protein: p.Pro1592=
Coding: c.4776A>G
MANE Select: NM_004638
dbSNP: rs2533849351
Type: single nucleotide variant
Location: chr6:31634292 (GRCh38)
Gene constraint: LOEUF 0.322 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 40.07
Residue 1592: the '4 x 57 aa type a repeats' region; the 'disordered' region

Full PRRC2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PRRC2A-related disorder

Similar variants

PRRC2A p.Pro1592Leu Likely benign same residue
PRRC2A p.Pro1592fs Uncertain significance ★ same residue
PRRC2A p.Lys308Arg Uncertain significance ⚠ same condition
PRRC2A c.391-6C>A Likely benign same condition
PRRC2A c.4720-6C>G Likely benign same condition
PRRC2A c.5624+9C>T Benign same condition
PRRC2A c.760-10C>G Likely benign same condition
PRRC2A c.*9C>T Likely benign same condition

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/prrc2a-p-pro1592 (accessed [today's date]).

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