SGF29

SAGA complex associated factor 29, the group of Tudor domain containing|ATAC complex|SAGA complex

Basic information

Region (hg38): 16:28553914-28591790

Previous symbols: [ "CCDC101" ]

Links

ENSG00000176476 ∙ NCBI:112869 ∙ OMIM:613374 ∙ HGNC:25156 ∙ Uniprot:Q96ES7 ∙ 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 SGF29 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGF29 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SGF29

This is a list of pathogenic ClinVar variants found in the SGF29 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28581079-G-C		not specified	Uncertain significance (Jun 24, 2022)
16-28581115-G-C		not specified	Uncertain significance (Apr 18, 2023)
16-28581138-A-T		not specified	Uncertain significance (Jul 11, 2023)
16-28584923-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-28585716-T-A		not specified	Uncertain significance (Nov 08, 2022)
16-28590840-C-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGF29	protein_coding	protein_coding	ENST00000317058	9	37876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00214	0.981	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.06	72	191	0.377	0.0000127	1879
Missense in Polyphen		6	31.289	0.19176		359
Synonymous	0.244	78	80.8	0.965	0.00000551	588
Loss of Function	2.09	7	16.0	0.437	6.80e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.000110	0.000109
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes (PubMed:19103755, PubMed:20850016, PubMed:26421618, PubMed:21685874, PubMed:26578293). SGF29 specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3) (PubMed:20850016, PubMed:26421618, PubMed:21685874, PubMed:26578293). In the SAGA-type complexes, SGF29 is required to recruit complexes to H3K4me (PubMed:20850016). Involved in the response to endoplasmic reticulum (ER) stress by recruiting the SAGA complex to H3K4me, thereby promoting histone H3 acetylation and cell survival (PubMed:23894581). {ECO:0000269|PubMed:19103755, ECO:0000269|PubMed:20850016, ECO:0000269|PubMed:21685874, ECO:0000269|PubMed:23894581, ECO:0000269|PubMed:26421618, ECO:0000269|PubMed:26578293}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.607
• ghis: 0.543

Essentials

• essential_gene_gene_trap: K

Mouse Genome Informatics

• Gene name: Sgf29
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: histone acetylation;histone H3 acetylation;RNA polymerase II preinitiation complex assembly;establishment of protein localization to chromatin
• Cellular component: SAGA complex;Ada2/Gcn5/Ada3 transcription activator complex;SAGA-type complex
• Molecular function: RNA polymerase II transcription regulator recruiting activity;protein binding;enzyme binding;methylated histone binding;protein N-terminus binding