SAP25

Sin3A associated protein 25

Basic information

Region (hg38): 7:100572228-100573900

Links

ENSG00000205307 ∙ NCBI:100316904 ∙ OMIM:619230 ∙ HGNC:41908 ∙ Uniprot:Q8TEE9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAP25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAP25 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			21	4		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	4	1

Variants in SAP25

This is a list of pathogenic ClinVar variants found in the SAP25 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-100572309-G-A		not specified	Uncertain significance (Sep 26, 2024)
7-100572318-A-G		not specified	Uncertain significance (May 16, 2024)
7-100572333-C-T		not specified	Uncertain significance (Jan 17, 2025)
7-100572352-T-C		not specified	Likely benign (May 14, 2024)
7-100572371-G-T		not specified	Uncertain significance (Nov 03, 2023)
7-100572405-G-C		not specified	Uncertain significance (May 30, 2023)
7-100572468-C-T		not specified	Uncertain significance (Nov 28, 2024)
7-100572493-C-T		not specified	Likely benign (Dec 05, 2024)
7-100572502-G-A		not specified	Uncertain significance (Jul 10, 2024)
7-100572510-C-T		not specified	Uncertain significance (Oct 01, 2024)
7-100572569-C-T		not specified	Uncertain significance (May 15, 2024)
7-100572655-T-G		not specified	Uncertain significance (May 27, 2022)
7-100572688-C-T		not specified	Uncertain significance (Sep 27, 2021)
7-100572689-G-A		not specified	Uncertain significance (Jul 19, 2023)
7-100572697-C-G		not specified	Uncertain significance (Mar 29, 2023)
7-100572697-C-T		not specified	Likely benign (Mar 27, 2023)
7-100572698-G-A		not specified	Uncertain significance (Apr 24, 2023)
7-100572714-C-G			Benign (Jun 27, 2018)
7-100572715-G-A		not specified	Likely benign (Sep 08, 2024)
7-100572740-C-A		not specified	Uncertain significance (Aug 07, 2024)
7-100572880-T-C		not specified	Uncertain significance (Apr 07, 2023)
7-100572911-C-T		not specified	Uncertain significance (Feb 22, 2023)
7-100572973-G-A		not specified	Uncertain significance (Sep 27, 2021)
7-100572976-C-T		not specified	Uncertain significance (Aug 02, 2021)
7-100572988-G-A		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAP25	protein_coding	protein_coding	ENST00000538735	4	1416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0850	0.772	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.360	58	66.2	0.876	0.00000423	1224
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sap25

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm