SAP25

protein-coding

Sin3A associated protein 25

Gene summary

Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001348680.2

Inheritance

—

ClinVar variants

U:34B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr7:100,572,228-100,573,900

External References & Databases

Ensembl (ENSG00000205307)

NCBI Gene (100316904)

Transcript & Mutation Effects

hg38 • Region Span ~1.7 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 SAP25 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001348680.2. 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					1 clinvar	1
missense			34 clinvar	7 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	7	1	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001348680.2	RefSeq	NP_001335609.1	6	MANE Select
ENST00000622764.3	Ensembl	ENSP00000481773.2	6	MANE Select
NM_001168682.3	RefSeq	NP_001162153.2	6	Standard
NM_001348677.2	RefSeq	NP_001335606.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000538735
Coding exons: 4
Length: 1416
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.360	58	66.2	0.876	0.00000423	1224
Missense (PolyPhen)		16	19.362	0.82637		270
Synonymous	-1.25	40	31.1	1.29	0.00000214	448
Loss of Function	1.08	2	4.47	0.447	1.91e-7	70

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the transcriptional repression mediated by the mSIN3A but not the N-CoR corepressor complex. {ECO:0000250}.;

Intolerance Scores

RVIS EVS: 0.32
RVIS percentile EVS: 72.94

Essentials

Essential (CRISPR): N
Essential (CRISPR2): 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