SAP30L

protein-coding

SAP30 like

Gene summary

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]

MANE transcript

NM_024632.6

Inheritance

—

ClinVar variants

U:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr5:154,445,997-154,461,053

External References & Databases

Ensembl (ENSG00000164576)

Transcript & Mutation Effects

hg38 • Region Span ~15.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAP30L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024632.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	22	0	0	22

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024632.6	RefSeq	NP_078908.1	4	MANE Select
ENST00000297109.11	Ensembl	ENSP00000297109.5	4	MANE Select
NM_001131062.2	RefSeq	NP_001124534.1	3	Standard
NM_001131063.2	RefSeq	NP_001124535.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
sap30l	Danio rerio	Structure: heart Quality: morphology abnormal

Gene / Model

Organism

Observed Phenotype

sap30l

Danio rerio

Structure: heart

Quality: morphology

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

NoRC negatively regulates rRNA expression
Negative epigenetic regulation of rRNA expression
Epigenetic regulation of gene expression
Gene expression (Transcription)
HDACs deacetylate histones

Biological Process

regulation of transcription, DNA-templated
histone deacetylation

Molecular Function

DNA binding
histone deacetylase activity
protein binding
zinc ion binding
phosphatidylinositol-5-phosphate binding

Cellular Component

histone deacetylase complex
nucleus
nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297109
Coding exons: 4
Length: 15098
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125747
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.797	78	100	0.776	0.00000509	1214
Missense (PolyPhen)		18	44.48	0.40468		524
Synonymous	1.56	29	41.8	0.694	0.00000233	325
Loss of Function	1.36	6	10.8	0.554	8.17e-7	95

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform 1: Functions as transcription repressor, probably via its interaction with histone deacetylase complexes (PubMed:16820529, PubMed:18070604). Involved in the functional recruitment of the class 1 Sin3-histone deacetylase complex (HDAC) to the nucleolus (PubMed:16820529). Binds DNA, apparently without sequence-specificity, and bends bound double-stranded DNA (PubMed:19015240). Binds phosphoinositol phosphates (phosphoinositol 3-phosphate, phosphoinositol 4-phosphate and phosphoinositol 5-phosphate) via the same basic sequence motif that mediates DNA binding and nuclear import (PubMed:19015240, PubMed:26609676). {ECO:0000269|PubMed:16820529, ECO:0000269|PubMed:18070604, ECO:0000269|PubMed:19015240, ECO:0000269|PubMed:26609676}.; FUNCTION: Isoform 3: Functions as transcription repressor; its activity is marginally lower than that of isoform 1. {ECO:0000269|PubMed:18070604}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.111
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.731

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium