ESS2

ess-2 splicing factor homolog, the group of Spliceosomal P complex

Basic information

Region (hg38): 22:19130279-19144684

Previous symbols: [ "DGCR13", "DGCR14" ]

Links

ENSG00000100056 ∙ NCBI:8220 ∙ OMIM:601755 ∙ HGNC:16817 ∙ Uniprot:Q96DF8 ∙ 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 ESS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESS2 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				7	2	9
missense			47		3	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding			27	1		28
Total	0	0	74	8	5

Variants in ESS2

This is a list of pathogenic ClinVar variants found in the ESS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-19131439-G-A		not specified	Uncertain significance (Feb 01, 2023)
22-19131497-G-A		not specified	Uncertain significance (Dec 12, 2023)
22-19131508-A-G		not specified	Uncertain significance (May 24, 2024)
22-19131529-G-A		not specified	Uncertain significance (Mar 25, 2022)
22-19131532-C-A		not specified	Uncertain significance (Nov 18, 2023)
22-19131532-C-T		not specified	Uncertain significance (Apr 08, 2024)
22-19131571-C-A		not specified	Uncertain significance (Apr 25, 2022)
22-19131580-A-G		not specified	Uncertain significance (Dec 16, 2023)
22-19131586-A-G		not specified	Uncertain significance (Oct 26, 2022)
22-19131596-C-A		not specified	Uncertain significance (Apr 25, 2022)
22-19131607-G-A		not specified	Uncertain significance (Aug 28, 2024)
22-19131617-T-C		not specified	Uncertain significance (Aug 19, 2024)
22-19131679-G-A		not specified	Uncertain significance (Apr 25, 2022)
22-19131764-C-T		not specified	Uncertain significance (Oct 16, 2024)
22-19131823-C-G		not specified	Uncertain significance (Sep 27, 2021)
22-19131877-C-T		not specified	Uncertain significance (Aug 27, 2024)
22-19131878-G-A		not specified	Uncertain significance (Jan 04, 2022)
22-19131940-T-C		not specified	Uncertain significance (Jan 26, 2022)
22-19131963-G-C		not specified	Uncertain significance (Dec 06, 2024)
22-19131974-A-C		not specified	Uncertain significance (Aug 10, 2023)
22-19132009-G-A		not specified	Uncertain significance (Jul 14, 2021)
22-19132031-G-A		not specified	Uncertain significance (Aug 15, 2023)
22-19132057-G-A		not specified	Uncertain significance (May 17, 2023)
22-19132107-G-A		not specified	Likely benign (Nov 09, 2024)
22-19132141-C-T		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESS2	protein_coding	protein_coding	ENST00000252137	10	14406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.44e-7	0.909	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.269	273	286	0.955	0.0000177	3042
Missense in Polyphen		95	117.54	0.80821		1205
Synonymous	-1.89	146	120	1.22	0.00000738	978
Loss of Function	1.71	14	22.8	0.613	0.00000113	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000565	0.000565
Ashkenazi Jewish	0.00	0.00
East Asian	0.000449	0.000435
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000449	0.000435
South Asian	0.000395	0.000392
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in pre-mRNA splicing. {ECO:0000250|UniProtKB:P34420}.

Recessive Scores

• pRec: 0.218

Intolerance Scores

• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.74

Haploinsufficiency Scores

• pHI: 0.102
• hipred: Y
• hipred_score: 0.590
• ghis: 0.572

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Ess2

Gene ontology

• Biological process: mRNA splicing, via spliceosome;nervous system development
• Cellular component: nucleus;catalytic step 2 spliceosome
• Molecular function: molecular_function;protein binding