SP9

Chr 2

Sp9 transcription factor

Also known as: ZNF990

NCBI Gene: 100131390ENSG00000217236UniProt: P0CG40

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

103
ClinVar variants
33
Pathogenic / LP
0.94
pLI score· haploinsufficient
1
Active trials
Clinical Summary— SP9
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.94). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
33 Pathogenic / Likely Pathogenic· 66 VUS of 103 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
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.
0.34LOEUF
pLI 0.940
Z-score 2.77
OE 0.00 (0.00–0.34)
Highly constrained

Highly LoF-intolerant (top ~10% 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 0.55 (0.47–0.64)
107 obs / 196.3 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.0.00 (0.00–0.34)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.55 (0.47–0.64)
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.0.97
0≤1.21.6
LoF obs/exp: 0 / 8.9Missense obs/exp: 107 / 196.3Syn Z: 0.19

ClinVar Variant Classifications

103 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic31
Likely Pathogenic2
VUS66
Likely Benign3
Conflicting1
31
Pathogenic
2
Likely Pathogenic
66
VUS
3
Likely Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
1
28
0
31
Likely Pathogenic
0
1
1
0
2
VUS
0
61
5
0
66
Likely Benign
0
0
0
3
3
Benign
0
0
0
0
0
Conflicting
—1
Total263343103

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

View in ClinVar →

Protein Context — Lollipop Plot

SP9 · protein map & ClinVar variants

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

Gene2Phenotype Curations

SP9-related neurodevelopmental disorder with or without epileptic encephalopathy

moderate
ADUndeterminedAltered Gene Product Structure
Dev. Disorders
G2P ↗
missense variantframeshift variant NMD escaping

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

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The Effect of Acupuncture and Physiotherapy on Patients with Knee Osteoarthritis: A Randomized Controlled Study.
Atalay SG et al.·Pain Physician
2021Cohort
The in vitro replication phenotype of hepatitis B virus (HBV) splice variants Sp3 and Sp9 and their impact on wild-type HBV replication.
McCoullough LC et al.·J Virol
2024
De novo variants in SP9 cause a novel form of interneuronopathy characterized by intellectual disability, autism spectrum disorder, and epilepsy with variable expressivity.
Tessarech M et al.·Genet Med
2024
Research on electroacupuncture parameters for knee osteoarthritis based on data mining.
Cai FH et al.·Eur J Med Res
2022Review
A strategic study of acupuncture for diabetic kidney disease based on meta-analysis and data mining.
Yu Y et al.·Front Endocrinol (Lausanne)
2024Meta-analysis
Efficacy of Low-Frequency Electroacupuncture on Urinary Retention After Spinal Anesthesia.
Olia M et al.·J Perianesth Nurs
2023
Acupuncture for benign prostatic hyperplasia in the elderly: A systematic review of acupoints.
Guo C et al.·Medicine (Baltimore)
2025Review
Efficacy of acupuncture and moxibustion therapy for simple obesity in adults: A meta-analysis of randomized controlled trials.
Yin Y et al.·Medicine (Baltimore)
2022Meta-analysis
Electrical Spinal Imaging: A noninvasive, high-resolution approach that enables electrophysiological mapping of the human spinal cord.
Gabrieli G et al.·PLoS Biol
2025
Visual analysis of acupuncture point selection patterns and related mechanisms in acupuncture for hypertension.
Li X et al.·Technol Health Care
2024Functional
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Hot FlashesMenopause Surgical

Acupuncture With/Without Self-acupressure for Post-oophorectomy Hot Flashes in BRCA Carriers

NOT YET RECRUITING
NCT05331209Phase NAShaare Zedek Medical CenterStarted 2026-01-01
AcupunctureAcupuncture-Acupressure

External Resources

Links to major genomics databases and tools