Is RNPC3 p.Ala70= (c.210C>A) pathogenic?

RNPC3 p.Ala70= (c.210C>A) is classified Likely benign in RNPC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-24). Absent from gnomAD v4.1.

How common is RNPC3 p.Ala70= (c.210C>A) in the general population?

RNPC3 p.Ala70= (c.210C>A) is absent from gnomAD v4.1 (gnomAD).

RNPC3 p.Ala70=

c.210C>A · VCV4904792

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.27	GERP -2.7, phastCons 1
Overall
CADD	8.433	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: RNPC3
Protein: p.Ala70=
Coding: c.210C>A
MANE Select: NM_017619
Type: single nucleotide variant
Location: chr1:103527712 (GRCh38)
Gene constraint: LOEUF 1.041 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.73 · 2 PDB
Residue 70: the rrm 1 domain; the 'necessary for interaction with pdcd7' region

Full RNPC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RNPC3 c.894-2A>G Likely pathogenic ★★ same type
RNPC3 p.Asn342His Uncertain significance ★★ ⚠ same type
RNPC3 c.359+16A>G Benign ★★ same type
RNPC3 p.Gly114= Benign ★★ same type
RNPC3 p.Arg205Ter Pathogenic ★ same type
RNPC3 c.1207+3A>G Uncertain significance ★ same type
RNPC3 p.Ala204Val Uncertain significance ★ ⚠ same type
RNPC3 p.Arg120Gly 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/rnpc3-p-ala70 (accessed [today's date]).

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