Is CD200 p.Thr138Ile (c.413C>T) pathogenic?

CD200 p.Thr138Ile (c.413C>T) is classified Uncertain significance in CD200 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-18). Ultra-rare (popmax 0.0227%, afr).

How common is CD200 p.Thr138Ile (c.413C>T) in the general population?

CD200 p.Thr138Ile (c.413C>T) is ultra-rare (popmax 0.0227%, afr) (gnomAD).

CD200 p.Thr138Ile

c.413C>T · VCV3998076

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0227%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.116	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.92	GERP -0.21, phastCons 0.41
Regional constraint	o/e 0.81	unconstrained · MANE · 28 kb · p 0.00055 · regional, not allelic
Overall
CADD	19.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0227% African / African-American · 17/74,830 alleles

Filtering AF 0.0144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0119%

Overall 0.00118% 19/1,611,264 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0227%	4,402
Middle Eastern	0.0164%	6,080
Remaining individualsnot grpmax-eligible	0.0016%	62,396

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: CD200
Protein: p.Thr138Ile
Coding: c.413C>T
MANE Select: NM_005944
Type: single nucleotide variant
Location: chr3:112345280 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 86.39
Residue 138: the ig-like v-type domain

Full CD200 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD200 c.12+2787T>A Uncertain significance ★ same type
CD200 p.Ala23Val Uncertain significance ★ same type
CD200 p.Arg261His Uncertain significance ★ same type
CD200 p.Arg3Thr Uncertain significance ★ same type
CD200 p.Asn157Ser Uncertain significance ★ same type
CD200 p.Asn55Lys Uncertain significance ★ same type
CD200 p.Asn81Lys Uncertain significance ★ same type
CD200 p.Gln42His 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/cd200-p-thr138ile (accessed [today's date]).

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