SAP130

Sin3A associated protein 130

Basic information

Region (hg38): 2:127941216-128028120

Links

ENSG00000136715 ∙ NCBI:79595 ∙ OMIM:609697 ∙ HGNC:29813 ∙ Uniprot:Q9H0E3 ∙ 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 SAP130 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAP130 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						0
missense			45			45
nonsense		1				1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	46	0	0

Variants in SAP130

This is a list of pathogenic ClinVar variants found in the SAP130 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-127942022-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-127942438-T-C		not specified	Uncertain significance (Feb 05, 2024)
2-127942513-C-T		not specified	Uncertain significance (May 31, 2022)
2-127945557-C-T		not specified	Uncertain significance (Dec 06, 2021)
2-127949881-C-T		not specified	Uncertain significance (Sep 25, 2023)
2-127949952-G-T		not specified	Uncertain significance (Sep 20, 2023)
2-127950186-C-T		not specified	Uncertain significance (May 16, 2023)
2-127950227-C-A		not specified	Uncertain significance (Jan 08, 2024)
2-127950340-G-C		not specified	Uncertain significance (Nov 12, 2021)
2-127950341-C-A		not specified	Uncertain significance (Nov 12, 2021)
2-127950385-T-C		not specified	Uncertain significance (Jul 21, 2021)
2-127950391-T-C		not specified	Uncertain significance (Jun 10, 2024)
2-127955001-T-C		not specified	Uncertain significance (Sep 27, 2021)
2-127955046-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-127955061-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-127955103-C-A		not specified	Uncertain significance (Nov 27, 2023)
2-127955124-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-127955166-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-127955211-T-C		not specified	Uncertain significance (Mar 24, 2023)
2-127955216-G-A		not specified	Uncertain significance (Dec 19, 2022)
2-127955244-C-T		not specified	Uncertain significance (Jan 29, 2024)
2-127955246-G-A		not specified	Uncertain significance (Dec 15, 2022)
2-127978079-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-127986827-G-C		not specified	Uncertain significance (Apr 15, 2024)
2-127986928-G-GGCCACAATTGTGGCAGATGGA			Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAP130	protein_coding	protein_coding	ENST00000357702	21	86904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000319	125739	0	2	125741	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.25	410	641	0.639	0.0000355	6943
Missense in Polyphen		140	286.73	0.48827		3111
Synonymous	0.301	232	238	0.975	0.0000139	2370
Loss of Function	6.06	3	48.6	0.0617	0.00000276	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. May function in the assembly and/or enzymatic activity of the mSin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes. {ECO:0000269|PubMed:12724404}.
• Pathway: NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0849

Intolerance Scores

• loftool: 0.0147
• rvis_EVS: -1.62
• rvis_percentile_EVS: 2.94

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.792
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sap130
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Zebrafish Information Network

• Gene name: sap130a
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nuclear speck;Sin3-type complex