Is PRRC2C p.Ser1950Phe (c.5849C>T) pathogenic?

PRRC2C p.Ser1950Phe (c.5849C>T) is classified Uncertain significance in PRRC2C (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-06). Absent from gnomAD v4.1.

How common is PRRC2C p.Ser1950Phe (c.5849C>T) in the general population?

PRRC2C p.Ser1950Phe (c.5849C>T) is absent from gnomAD v4.1 (gnomAD).

PRRC2C p.Ser1950Phe

c.5849C>T · VCV3783921

Uncertain significance Single submitter

Classification

Uncertain significance

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.
REVEL	0.131	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.5	GERP 1.8, phastCons 0.13
Regional constraint	o/e 0.95	unconstrained · MANE · 21 kb · p 0.17 · regional, not allelic
Overall
CADD	21.1	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: PRRC2C
Protein: p.Ser1950Phe
Coding: c.5849C>T
MANE Select: NM_001387844
Type: single nucleotide variant
Location: chr1:171557961 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Residue 1950: 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-ser1950phe (accessed [today's date]).

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