SOX11

Chr 2AD

SRY-box transcription factor 11

Also known as: CSS9, IDDMOH, MRD27

NCBI Gene: 6664ENSG00000176887UniProt: P35716

This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The protein may function in the developing nervous system and play a role in tumorigenesis. [provided by RefSeq, Jul 2008]

Primary Disease Associations & Inheritance

Intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadismMIM #615866
AD
471
ClinVar variants
108
Pathogenic / LP
0.86
pLI score
0
Active trials
Clinical Summary— SOX11
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.86) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
108 Pathogenic / Likely Pathogenic· 223 VUS of 471 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.44LOEUF
pLI 0.858
Z-score 2.76
OE 0.09 (0.03–0.44)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.26Z-score
OE missense 0.59 (0.52–0.68)
146 obs / 245.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.09 (0.03–0.44)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.59 (0.52–0.68)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.35
0≤1.21.6
LoF obs/exp: 1 / 10.8Missense obs/exp: 146 / 245.6Syn Z: -2.95

ClinVar Variant Classifications

471 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic43
Likely Pathogenic65
VUS223
Likely Benign92
Benign21
Conflicting27
43
Pathogenic
65
Likely Pathogenic
223
VUS
92
Likely Benign
21
Benign
27
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
5
9
29
0
43
Likely Pathogenic
8
49
8
0
65
VUS
3
166
24
30
223
Likely Benign
0
17
8
67
92
Benign
0
10
3
8
21
Conflicting
—27
Total1625172105471

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

View in ClinVar →

Protein Context — Lollipop Plot

SOX11 · protein map & ClinVar variants

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

Gene2Phenotype Curations

SOX11-related neurodevelopmental disorder

definitive
ADUndeterminedAbsent Gene Product, Altered Gene Product Structure
Dev. Disorders
G2P ↗
missense variantinframe deletioninframe insertion

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
SRY-BOX 11; SOX11
MIM #600898 · *

Intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism

MIM #615866

Molecular basis of disorder known

Autosomal dominant
📖
GeneReview available — SOX11
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Molecular Pathogenesis of Mantle Cell Lymphoma.
Navarro A et al.·Hematol Oncol Clin North Am
2020Review
Integrative Single-Cell and Spatial Transcriptomics Analysis Reveals ECM-remodeling Cancer-associated Fibroblast-Derived POSTN as a Key Mediator in Pancreatic Ductal Adenocarcinoma Progression.
Wu Y et al.·Int J Biol Sci
2025Functional
How I manage mantle cell lymphoma: indolent versus aggressive disease.
Wilson MR et al.·Br J Haematol
2023Review
High-risk MCL: recognition and treatment.
Jain P et al.·Blood
2025Review
Mantle cell lymphoma in 2022-A comprehensive update on molecular pathogenesis, risk stratification, clinical approach, and current and novel treatments.
Jain P et al.·Am J Hematol
2022
Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis.
Luo Z et al.·Nature
2022
Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome.
Vasko A et al.·Genes (Basel)
2021
Mantle cell lymphoma: 2019 update on the diagnosis, pathogenesis, prognostication, and management.
Jain P et al.·Am J Hematol
2019Review
SOX11, CD70, and Treg cells configure the tumor-immune microenvironment of aggressive mantle cell lymphoma.
Balsas P et al.·Blood
2021
Subtyping Burkitt Lymphoma by DNA Methylation.
Glaser S et al.·Genes Chromosomes Cancer
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
SOX11 Is Regulated by EGFR-STAT3 and Promotes Epithelial-Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma.
Peng J et al.·Cells
2026🔓 Open Access
Sox11 overexpression restores embryonic pro-growth transcription in mature corticospinal tract neurons.
Batsel E et al.·Sci Rep
2025🔓 Open Access
SOX11 modulates BCR signaling through the PAX5/CD19 axis for therapeutic targeting in BTK-resistant mantle cell lymphoma.
Dutta RP et al.·Blood Adv
2025🔓 Open Access
Development and validation of a pathomics model to predict SOX11 expression and prognosis in hepatocellular carcinoma.
Liu S et al.·Transl Cancer Res
2025🔓 Open AccessFunctional
SOX11 is frequently expressed in ETV6::NTRK3-rearranged infantile fibrosarcoma and congenital mesoblastic nephroma.
Malik F et al.·Virchows Arch
2025
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools