Is PRRC2C p.Val50= (c.150C>T) pathogenic?

PRRC2C p.Val50= (c.150C>T) is classified Likely benign in PRRC2C (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-01). Ultra-rare (popmax 0.0331%, nfe).

How common is PRRC2C p.Val50= (c.150C>T) in the general population?

PRRC2C p.Val50= (c.150C>T) is ultra-rare (popmax 0.0331%, nfe) (gnomAD).

PRRC2C p.Val50=

c.150C>T · VCV3388016

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0331%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.4	GERP -3.5, phastCons 1
Overall
CADD	12.58	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0331% European (non-Finnish) · 390/1,179,532 alleles

Filtering AF 0.0303% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0293%

Overall 0.0717% 1,157/1,612,924 alleles · ultra-rare exomes 1,051/1,460,792 · genomes 106/152,132 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	2.23%	45
Amishnot grpmax-eligible	0.548%	182
Remaining individualsnot grpmax-eligible	0.146%	686
European (non-Finnish)grpmax	0.0331%	3,024
Admixed American	0.0117%	8,549
Finnishnot grpmax-eligible	0.00313%	31,992
East Asian	0.00223%	44,866
African / African-American	0.00134%	74,852

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: PRRC2C
Protein: p.Val50=
Coding: c.150C>T
MANE Select: NM_001387844
Type: single nucleotide variant
Location: chr1:171513032 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Residue 50: the 'disordered' region

Full PRRC2C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PRRC2C c.1055+2T>C Uncertain significance ★ same type
PRRC2C p.Ala104Thr Uncertain significance ★ same type
PRRC2C p.Ala1120Thr Uncertain significance ★ same type
PRRC2C p.Ala1762Ser Uncertain significance ★ same type
PRRC2C p.Ala1774Ser Uncertain significance ★ same type
PRRC2C p.Ala1785Val Uncertain significance ★ same type
PRRC2C p.Ala1927Thr Uncertain significance ★ same type
PRRC2C p.Ala1930Val 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/prrc2c-p-val50 (accessed [today's date]).

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