ESS2

protein-coding

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

Gene summary

This gene is located within the minimal DGS critical region (MDGCR) thought to contain the gene(s) responsible for a group of developmental disorders. These disorders include DiGeorge syndrome, velocardiofacial syndrome, conotruncal anomaly face syndrome, and some familial or sporadic conotruncal cardiac defects which have been associated with microdeletion of 22q11.2. The encoded protein may be a component of C complex spliceosomes, and the orthologous protein in the mouse localizes to the nucleus. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]

Previous symbols:

DGCR13
DGCR14

MANE transcript

NM_022719.3

Inheritance

—

ClinVar variants

U:105B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr22:19,130,279-19,144,684

External References & Databases

Ensembl (ENSG00000100056)

Transcript & Mutation Effects

hg38 • Region Span ~14.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ESS2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 100

not providedTotal: 17

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022719.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	1 clinvar	9
missense			100 clinvar	1 clinvar	4 clinvar	105
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	105	9	5	119

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022719.3	RefSeq	NP_073210.1	10	MANE Select
ENST00000252137.11	Ensembl	ENSP00000252137.6	10	MANE Select
ENST00000434568.5	Ensembl	ENSP00000388524.1	7	Standard
ENST00000909110.1	Ensembl	ENSP00000579169.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splicing, via spliceosome
nervous system development

Molecular Function

molecular_function
protein binding

Cellular Component

nucleus
catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252137
Coding exons: 10
Length: 14406
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125748
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.269	273	286	0.955	0.0000177	3042
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00050	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00045	0.00044	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00040	0.00039	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): E