SSX2IP

Chr 1

SSX family member 2 interacting protein

Also known as: ADIP, hMsd1

NCBI Gene: 117178ENSG00000117155UniProt: Q9Y2D8

The protein functions as a centrosome maturation factor and regulator of cell adhesion junctions, maintaining pericentriolar material integrity, promoting proper microtubule nucleation at spindle poles, and playing essential roles in ciliogenesis by recruiting key proteins to cilia. Mutations cause autosomal recessive developmental epileptic encephalopathy with early infantile onset, characterized by severe seizures and developmental delay. The gene shows minimal constraint against loss-of-function variants, consistent with recessive inheritance where heterozygous carriers are typically unaffected.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
2
Pubs (1 yr)
16
P/LP submissions
0%
P/LP missense
0.79
LOEUF
DN
Mechanism· predicted
Clinical Summary— SSX2IP
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
16 unique Pathogenic / Likely Pathogenic· 80 VUS of 115 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.79LOEUF
pLI 0.000
Z-score 2.54
OE 0.55 (0.38–0.79)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.37Z-score
OE missense 0.94 (0.85–1.04)
292 obs / 310.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.55 (0.38–0.79)
0≤0.351.4
Missense OE0.94 (0.85–1.04)
0≤0.61.4
Synonymous OE0.93
0≤1.21.6
LoF obs/exp: 20 / 36.6Missense obs/exp: 292 / 310.4Syn Z: 0.61
DN
0.6744th %ile
GOF
0.5758th %ile
LOF
0.3940th %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

115 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic2
VUS80
Likely Benign2
14
Pathogenic
2
Likely Pathogenic
80
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
14
0
14
Likely Pathogenic
0
0
2
0
2
VUS
0
79
1
0
80
Likely Benign
0
2
0
0
2
Benign
0
0
0
0
0
Total08117098

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

View in ClinVar →

Protein Context — Lollipop Plot

SSX2IP · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients