Is CP p.Arg310Cys (c.928C>T) pathogenic?

CP p.Arg310Cys (c.928C>T) is classified Uncertain significance in CP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-28). AlphaMissense: likely benign (0.218); Ultra-rare (popmax 0.0147%, afr).

How common is CP p.Arg310Cys (c.928C>T) in the general population?

CP p.Arg310Cys (c.928C>T) is ultra-rare (popmax 0.0147%, afr) (gnomAD).

What do computational predictors say about CP p.Arg310Cys (c.928C>T)?

AlphaMissense predicts likely benign (score 0.218) — an in-silico prediction, not a clinical call.

CP p.Arg310Cys

c.928C>T · rs767161351 · VCV3233723

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.218 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0147%, afr)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.218	likely benign
REVEL	0.828	moderately pathogenic-leaning
SaProt	LLR -13.36	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.2	GERP 2.2, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 23 kb · p 0.56 · regional, not allelic
Overall
CADD	28.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0147% African / African-American · 11/75,006 alleles

Filtering AF 0.00814% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00633%

Overall 0.00112% 18/1,613,932 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0147%	6,819
European (non-Finnish)	0.000593%	168,555

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: CP
Protein: p.Arg310Cys
Coding: c.928C>T
MANE Select: NM_000096
dbSNP: rs767161351
Type: single nucleotide variant
Location: chr3:149207471 (GRCh38)
Gene constraint: LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.79 · 4 PDB
Residue 310: a β-strand; the plastocyanin-like 2 domain; a disulfide bond

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

Similar variants

CP p.Arg310Gly Likely pathogenic ★ ⚠ same residue
CP p.Arg310His Conflicting classifications of pathogenicity ★ ⚠ same residue
CP c.1208+1G>A Pathogenic ★★ same type
CP c.2879-1G>T Likely pathogenic ★★ same type
CP p.Arg901Ter Pathogenic ★★ same type
CP p.Gly195Arg Likely pathogenic ★★ same type
CP p.Gly650Arg Pathogenic/Likely pathogenic ★★ same type
CP p.Gly708Ser Pathogenic ★★ 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/cp-p-arg310cys (accessed [today's date]).

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