SAP30L

Chr 5

SAP30 like

Also known as: NS4ATP2

NCBI Gene: 79685ENSG00000164576UniProt: Q9HAJ7

Enables several functions, including non-sequence-specific DNA binding activity, bending; phosphatidylinositol phosphate binding activity; and zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of histone deacetylase complex. [provided by Alliance of Genome Resources, Apr 2025]

0
Active trials
12
Pathogenic / LP
36
ClinVar variants
1
Pubs (1 yr)
0.8
Missense Z
1.09
LOEUF
Clinical Summary— SAP30L
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
12 Pathogenic / Likely Pathogenic· 23 VUS of 36 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.09LOEUF
pLI 0.001
Z-score 1.36
OE 0.55 (0.30–1.09)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.80Z-score
OE missense 0.78 (0.65–0.94)
78 obs / 100.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.55 (0.30–1.09)
0≤0.351.4
Missense OE0.78 (0.65–0.94)
0≤0.61.4
Synonymous OE0.69
0≤1.21.6
LoF obs/exp: 6 / 10.8Missense obs/exp: 78 / 100.5Syn Z: 1.56

ClinVar Variant Classifications

36 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic12
VUS23
Likely Benign1
12
Pathogenic
23
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
12
0
12
Likely Pathogenic
0
0
0
0
0
VUS
0
21
2
0
23
Likely Benign
0
0
1
0
1
Benign
0
0
0
0
0
Total02115036

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

View in ClinVar →

SAP30L · 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
Landmark / reviewRecent case evidence
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 3 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