CD200R1L

Chr 3

CD200 receptor 1 like

Also known as: CD200R2, CD200RLa

NCBI Gene: 344807 ENSG00000206531 UniProt: Q6Q8B3

CD200R1L encodes a predicted signaling receptor that may function as a receptor for the CD200/OX2 cell surface glycoprotein and is involved in regulation of neuroinflammatory responses. The gene shows low constraint against loss-of-function variants (LOEUF 0.936), and no definitive human disease associations have been established for pathogenic variants in this gene. Clinical significance of CD200R1L variants in pediatric neurological conditions remains to be determined.

ResearchSummary from RefSeq, UniProt

Predicted to enable signaling receptor activity. Predicted to be involved in regulation of neuroinflammatory response. Predicted to be located in cell surface and membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

MultiplemechanismLOEUF 0.94

Clinical Summary— CD200R1L

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

43 VUS of 49 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.94LOEUF

pLI 0.003

Z-score 1.73

OE 0.47 (0.26–0.94)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

-0.41Z-score

OE missense 1.10 (0.96–1.25)

160 obs / 145.9 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.47 (0.26–0.94)

0≤0.351.4

Missense OE?1.10 (0.96–1.25)

0≤0.61.4

Synonymous OE?1.32

0≤1.21.6

LoF obs/exp: 6 / 12.6Missense obs/exp: 160 / 145.9Syn Z: -1.86

This gene — mechanism propensity

0.7326th %ile

GOF

0.7127th %ile

LOF

0.2580th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

49 submitted variants in ClinVar

ClinVar

Classification Summary

VUS43

Likely Benign2

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	43	43
Likely Benign	2	2
Benign	0	0
Total	45	45

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

27 pathogenic / likely-pathogenic (of 31) ClinVar copy-number / structural variants overlap CD200R1L — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →