Is CD2 p.Thr28Met (c.83C>T) pathogenic?

CD2 p.Thr28Met (c.83C>T) is classified Uncertain significance in CD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-26). AlphaMissense: likely benign (0.1319); Ultra-rare (popmax 0.0332%, mid).

How common is CD2 p.Thr28Met (c.83C>T) in the general population?

CD2 p.Thr28Met (c.83C>T) is ultra-rare (popmax 0.0332%, mid) (gnomAD).

What do computational predictors say about CD2 p.Thr28Met (c.83C>T)?

AlphaMissense predicts likely benign (score 0.1319) — an in-silico prediction, not a clinical call.

CD2 p.Thr28Met

c.83C>T · rs369310866 · VCV2390185

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1319 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0332%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1319	likely benign
REVEL	0.206	benign-leaning
SaProt	LLR -8.35	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 -6.8	GERP -2.5
Regional constraint	o/e 1.00	unconstrained · MANE · 14 kb · p 0.97 · regional, not allelic
Overall
CADD	0.032	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 0.0332% Middle Eastern · 2/6,028 alleles

Filtering AF 0.0171% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0136%

Overall 0.0046% 74/1,607,080 alleles · ultra-rare exomes 69/1,454,944 · genomes 5/152,136 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0332%	3,014
East Asian	0.029%	3,451
Remaining individualsnot grpmax-eligible	0.0113%	8,879
South Asian	0.00783%	12,773
Admixed American	0.00514%	19,443
European (non-Finnish)	0.00348%	28,732
Finnishnot grpmax-eligible	0.00157%	63,884

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: CD2
Protein: p.Thr28Met
Coding: c.83C>T
MANE Select: NM_001767
dbSNP: rs369310866
Type: single nucleotide variant
Location: chr1:116754652 (GRCh38)
Gene constraint: LOEUF 1.143 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.25 · 7 PDB
Residue 28: an α-helix; the ig-like v-type domain

Full CD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD2 p.Ala270Thr Uncertain significance ★ ⚠ same type
CD2 p.Ala292Ser Uncertain significance ★ ⚠ same type
CD2 p.Ala342Thr Uncertain significance ★ ⚠ same type
CD2 p.Arg129Lys Uncertain significance ★ ⚠ same type
CD2 p.Arg129Trp Uncertain significance ★ ⚠ same type
CD2 p.Arg243Gln Uncertain significance ★ ⚠ same type
CD2 p.Arg243Leu Uncertain significance ★ ⚠ same type
CD2 p.Arg263Gln 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/cd2-p-thr28met (accessed [today's date]).

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