SSX2IP

Chr 1

SSX family member 2 interacting protein

Also known as: ADIP, hMsd1

NCBI Gene: 117178 ENSG00000117155 UniProt: Q9Y2D8 OMIM: 608690

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.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a protein that binds the cancer-testis antigen Synovial Sarcoma X breakpoint 2 protein. The encoded protein may regulate the activity of Synovial Sarcoma X breakpoint 2 protein in malignant cells. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Oct 2009]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.79

LOEUF

Mechanism· predicted

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 OE?0.55 (0.38–0.79)

0≤0.351.4

Missense OE?0.94 (0.85–1.04)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 20 / 36.6Missense obs/exp: 292 / 310.4Syn Z: 0.61

Background carrier burden — how many people carry a rare variant somewhere in SSX2IP?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

711 rare PASS variants

Rare truncating (LoF)

1 in 1,300

140 rare PASS variants

Rare synonymous (reference)

1 in 220

258 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SSX2IP. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 140	1 in 1,400
South Asian	~43k	1 in 100	1 in 880
Remaining (unassigned)	~30k	1 in 74	1 in 1,800
European (Finnish)	~27k	1 in 540	1 in 3,800
Admixed American	~22k	1 in 78	1 in 1,300
African / African American	~21k	1 in 85	1 in 1,300
East Asian	~20k	1 in 84	1 in 1,600
Ashkenazi Jewish	~13k	1 in 190	1 in 1,500
Middle Eastern	~2,884	1 in 92	≈ 1 in 960

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 13 coding exons well covered in gnomAD exomes and genomes.? see exons ↓