TNFSF11

Chr 13AR

TNF superfamily member 11

Also known as: CD254, ODF, OPGL, OPTB2, RANKL, TNLG6B, TRANCE, hRANKL2

The protein functions as a cytokine that binds to osteoprotegerin and RANK receptor, serving as a key factor for osteoclast differentiation and activation, and also regulates T-cell dependent immune responses and dendritic cell survival. Mutations cause autosomal recessive osteopetrosis type 2, characterized by defective bone resorption due to absent or dysfunctional osteoclasts, leading to dense but brittle bones and potential complications including bone marrow failure and cranial nerve compression. This gene shows low constraint against loss-of-function variants (pLI 0.005), consistent with the recessive inheritance pattern where heterozygous carriers are typically unaffected.

OMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismARLOEUF 0.851 OMIM phenotype
Clinical SummaryTNFSF11
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Gene-Disease Validity (ClinGen)
autosomal recessive osteopetrosis 2 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
54 unique Pathogenic / Likely Pathogenic· 129 VUS of 321 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.85LOEUF
pLI 0.005
Z-score 1.96
OE 0.43 (0.240.85)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.93Z-score
OE missense 0.80 (0.700.92)
139 obs / 173.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.43 (0.240.85)
00.351.4
Missense OE0.80 (0.700.92)
00.61.4
Synonymous OE1.16
01.21.6
LoF obs/exp: 6 / 13.9Missense obs/exp: 139 / 173.4Syn Z: -1.02
DN
0.7034th %ile
GOF
0.5268th %ile
LOF
0.3453th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction 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

321 submitted variants in ClinVar

Classification Summary

Pathogenic53
Likely Pathogenic1
VUS129
Likely Benign109
Benign18
Conflicting9
53
Pathogenic
1
Likely Pathogenic
129
VUS
109
Likely Benign
18
Benign
9
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
1
50
0
53
Likely Pathogenic
1
0
0
0
1
VUS
1
91
34
3
129
Likely Benign
0
2
24
83
109
Benign
0
2
12
4
18
Conflicting
9
Total49612090319

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

View in ClinVar →

Protein Context — Lollipop Plot

TNFSF11 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
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