SPTY2D1

SPT2 chromatin protein domain containing 1

Basic information

Region (hg38): 11:18606403-18634791

Links

ENSG00000179119 ∙ NCBI:144108 ∙ ∙ HGNC:26818 ∙ Uniprot:Q68D10 ∙ 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 SPTY2D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPTY2D1 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			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	35	2	0

Variants in SPTY2D1

This is a list of pathogenic ClinVar variants found in the SPTY2D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18609865-C-T		not specified	Uncertain significance (Nov 17, 2022)
11-18609866-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-18609880-T-C		not specified	Uncertain significance (Aug 09, 2021)
11-18612342-T-C		not specified	Uncertain significance (Sep 30, 2021)
11-18612423-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-18612431-T-C		not specified	Uncertain significance (Jan 02, 2024)
11-18612478-C-A		not specified	Uncertain significance (Mar 14, 2023)
11-18612486-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-18614661-A-T		not specified	Uncertain significance (Feb 17, 2024)
11-18614703-A-T		not specified	Uncertain significance (Oct 26, 2021)
11-18614769-G-A		not specified	Uncertain significance (Mar 23, 2023)
11-18614805-C-T		not specified	Uncertain significance (Oct 12, 2022)
11-18614844-C-T		not specified	Uncertain significance (Sep 26, 2023)
11-18614860-G-A		not specified	Uncertain significance (Dec 15, 2023)
11-18614874-C-T		not specified	Uncertain significance (Apr 28, 2023)
11-18614878-C-G		not specified	Uncertain significance (Dec 28, 2023)
11-18614950-A-G		not specified	Uncertain significance (Aug 28, 2023)
11-18614958-G-C		not specified	Uncertain significance (Feb 05, 2024)
11-18615000-G-C		not specified	Uncertain significance (Jan 19, 2022)
11-18615007-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-18615084-G-A		not specified	Uncertain significance (May 22, 2023)
11-18615207-A-T		not specified	Uncertain significance (Jun 06, 2023)
11-18615318-G-A		not specified	Uncertain significance (Feb 09, 2023)
11-18615336-C-A		not specified	Uncertain significance (Nov 21, 2023)
11-18615372-C-T		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPTY2D1	protein_coding	protein_coding	ENST00000336349	6	28391

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0552	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	319	375	0.851	0.0000202	4470
Missense in Polyphen		42	66.336	0.63314		712
Synonymous	-0.141	131	129	1.02	0.00000644	1355
Loss of Function	4.35	5	31.2	0.160	0.00000247	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone chaperone that stabilizes pre-existing histone tetramers and regulates replication-independent histone exchange on chromatin (PubMed:26109053). Required for normal chromatin refolding in the coding region of transcribed genes, and for the suppression of spurious transcription (PubMed:26109053). Binds DNA and histones and promotes nucleosome assembly (in vitro) (PubMed:23378026, PubMed:26109053). Facilitates formation of tetrameric histone complexes containing histone H3 and H4 (PubMed:26109053). Modulates RNA polymerase 1-mediated transcription (By similarity). Binds DNA, with a preference for branched DNA species, such as Y-form DNA and Holliday junction DNA (PubMed:23378026). {ECO:0000250|UniProtKB:E1BUG7, ECO:0000269|PubMed:23378026}.

Intolerance Scores

• loftool: 0.423
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.58

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.469
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.499

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spty2d1

Gene ontology

• Biological process: nucleosome assembly;regulation of transcription, DNA-templated;regulation of chromatin assembly;histone exchange
• Cellular component: cellular_component;nucleolus
• Molecular function: RNA polymerase I core binding;DNA binding;histone binding