Is CD86 p.Ala310Thr (c.928G>A) pathogenic?

CD86 p.Ala310Thr (c.928G>A) is classified Benign in CD86 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-11-10). AlphaMissense: likely benign (0.0756); Common (popmax 63.4%, eas) — too common for a highly-penetrant pathogenic allele.

What do computational predictors say about CD86 p.Ala310Thr (c.928G>A)?

AlphaMissense predicts likely benign (score 0.0756) — an in-silico prediction, not a clinical call.

CD86 p.Ala310Thr

Q: How common is CD86 p.Ala310Thr (c.928G>A) in the general population?

CD86 p.Ala310Thr (c.928G>A) is common (popmax 63.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.928G>A · rs1129055 · VCV1227026

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0756 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 63.4%, eas) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0756	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -5.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 1.6, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 64 kb · p 0.048 · regional, not allelic
Overall
CADD	8.662	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 63.4% East Asian · 28,402/44,778 alleles

Filtering AF 62.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 62.6%

Overall 28.5% 457,629/1,604,162 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	63.4%	2
South Asian	44.3%	2
Finnishnot grpmax-eligible	32.1%	3
Remaining individualsnot grpmax-eligible	29.4%	3
Middle Eastern	27.8%	4
European (non-Finnish)	27.1%	4
Ashkenazi Jewishnot grpmax-eligible	26.4%	4
Amishnot grpmax-eligible	24%	4
Admixed American	18.1%	6
African / African-American	17.1%	6

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.Ala310Thr
Coding: c.928G>A
MANE Select: NM_175862
dbSNP: rs1129055
Type: single nucleotide variant
Location: chr3:122119472 (GRCh38)
Gene constraint: LOEUF 0.555 · pLI 0.93 (gnomAD)
Structure: AlphaFold pLDDT 80.10 · 7 PDB
Residue 310: a UniProt-annotated variant site (in); the 'disordered' region

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

Similar variants

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
CD86 p.Gln311Glu Uncertain significance ★ ⚠ same type
CD86 p.Glu181Ala 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-ala310thr (accessed [today's date]).

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