Is PRRC2A p.Arg1370= (c.4110C>T) pathogenic?

PRRC2A p.Arg1370= (c.4110C>T) is classified Benign in PRRC2A (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-10). Low-frequency (popmax 1.39%, afr); Associated with PRRC2A-related disorder.

What condition is associated with PRRC2A p.Arg1370= (c.4110C>T)?

PRRC2A p.Arg1370= (c.4110C>T) is associated with PRRC2A-related disorder (ClinVar).

How common is PRRC2A p.Arg1370= (c.4110C>T) in the general population?

PRRC2A p.Arg1370= (c.4110C>T) is low-frequency (popmax 1.39%, afr) (gnomAD).

PRRC2A p.Arg1370=

c.4110C>T · rs9501151 · VCV3042283

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.39%, afr)

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 -4.4	GERP -3.4
Overall
CADD	5.336	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.39% African / African-American · 1,040/75,020 alleles

Filtering AF 1.32% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.29%

Overall 0.0957% 1,544/1,613,050 alleles · low-frequency exomes 903/1,460,782 · genomes 641/152,268 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.39%	72
Admixed American	0.202%	496
Remaining individualsnot grpmax-eligible	0.165%	607
Middle Eastern	0.116%	866
South Asian	0.0318%	3,141
European (non-Finnish)	0.0207%	4,836

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: PRRC2A
Protein: p.Arg1370=
Coding: c.4110C>T
MANE Select: NM_004638
dbSNP: rs9501151
Type: single nucleotide variant
Location: chr6:31632783 (GRCh38)
Gene constraint: LOEUF 0.322 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 40.07
Residue 1370: 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.Arg1370His 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
PRRC2A p.Ala1222= 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-arg1370 (accessed [today's date]).

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