Is CD86 p.Arg312Cys (c.934C>T) pathogenic?

CD86 p.Arg312Cys (c.934C>T) is classified Likely benign in CD86 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-22). AlphaMissense: likely benign (0.073); Rare (popmax 0.107%, sas).

How common is CD86 p.Arg312Cys (c.934C>T) in the general population?

CD86 p.Arg312Cys (c.934C>T) is rare (popmax 0.107%, sas) (gnomAD).

What do computational predictors say about CD86 p.Arg312Cys (c.934C>T)?

AlphaMissense predicts likely benign (score 0.073) — an in-silico prediction, not a clinical call.

CD86 p.Arg312Cys

c.934C>T · rs201148004 · VCV3140701

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.073 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.107%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.073	likely benign
REVEL	0.11	moderately benign-leaning
SaProt	LLR -6.94	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.20	acceptor loss, 40 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -1.3	GERP -3.1
Regional constraint	o/e 0.90	unconstrained · MANE · 64 kb · p 0.048 · regional, not allelic
Overall
CADD	0.047	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 0.107% South Asian · 97/90,960 alleles

Filtering AF 0.0894% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.083%

Overall 0.00993% 160/1,611,274 alleles · rare exomes 146/1,459,104 · genomes 14/152,170 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.107%	938
Middle Eastern	0.0164%	6,082
Remaining individualsnot grpmax-eligible	0.00961%	10,401
European (non-Finnish)	0.00425%	23,553
African / African-American	0.00401%	24,952
Admixed American	0.00334%	29,983
East Asian	0.00223%	44,850

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: CD86
Protein: p.Arg312Cys
Coding: c.934C>T
MANE Select: NM_175862
dbSNP: rs201148004
Type: single nucleotide variant
Location: chr3:122119478 (GRCh38)
Gene constraint: LOEUF 0.555 · pLI 0.93 (gnomAD)
Structure: AlphaFold pLDDT 80.10 · 7 PDB
Residue 312: the 'disordered' region

Full CD86 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD86 p.Arg312His Likely benign ★ same residue
CD86 p.Ala310Thr Benign ★★ same type
CD86 p.Asp323Asn Benign ★★ same type
CD86 p.Ala24Val Uncertain significance ★ ⚠ same type
CD86 p.Arg277Cys Uncertain significance ★ ⚠ same type
CD86 p.Arg277His Uncertain significance ★ ⚠ same type
CD86 p.Arg306Ile Uncertain significance ★ ⚠ same type
CD86 p.Asp104Glu 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/cd86-p-arg312cys (accessed [today's date]).

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