Is CD8B p.Arg201Gln (c.602G>A) pathogenic?

CD8B p.Arg201Gln (c.602G>A) is classified Uncertain significance in CD8B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-27). AlphaMissense: likely benign (0.1051); Very rare (popmax 0.00593%, sas).

How common is CD8B p.Arg201Gln (c.602G>A) in the general population?

CD8B p.Arg201Gln (c.602G>A) is very rare (popmax 0.00593%, sas) (gnomAD).

What do computational predictors say about CD8B p.Arg201Gln (c.602G>A)?

AlphaMissense predicts likely benign (score 0.1051) — an in-silico prediction, not a clinical call.

CD8B p.Arg201Gln

c.602G>A · VCV3488205

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1051 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00593%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1051	likely benign
REVEL	0.154	moderately benign-leaning
SaProt	LLR -7.05	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 1.1	phastCons 1
Regional constraint	o/e 0.72	unconstrained · MANE · 20 kb · p 4.9e-06 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00593% South Asian · 5/84,254 alleles

Filtering AF 0.00233% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00146%

Overall 0.00244% 38/1,556,316 alleles · very rare exomes 32/1,404,142 · genomes 6/152,174 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00593%	16,851
African / African-American	0.00409%	24,437
European (non-Finnish)	0.00244%	41,062
East Asian	0.00242%	41,308
Admixed American	0.00194%	51,592

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: CD8B
Protein: p.Arg201Gln
Coding: c.602G>A
MANE Select: NM_004931
Type: single nucleotide variant
Location: chr2:86844940 (GRCh38)
Gene constraint: LOEUF 0.764 · pLI 0.42 (gnomAD)
Structure: AlphaFold pLDDT 82.03

Full CD8B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD8B p.Ala190Thr Uncertain significance ★ ⚠ same type
CD8B p.Ala60Thr Uncertain significance ★ ⚠ same type
CD8B p.Arg156Trp Uncertain significance ★ ⚠ same type
CD8B p.Arg203Cys Uncertain significance ★ ⚠ same type
CD8B p.Arg51His Uncertain significance ★ ⚠ same type
CD8B p.Arg98Gln Uncertain significance ★ ⚠ same type
CD8B p.Arg98Leu Uncertain significance ★ ⚠ same type
CD8B p.Gln23Lys 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/cd8b-p-arg201gln (accessed [today's date]).

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