CECR2

protein-coding

CECR2 histone acetyl-lysine reader, the group of Bromodomain containing

Gene summary

This gene encodes a bromodomain-containing protein that is involved in chromatin remodeling, and may additionally play a role in DNA damage response. The encoded protein functions as part of an ATP-dependent complex that is involved in neurulation. This gene is a candidate gene for Cat Eye Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

MANE transcript

NM_001290047.2

Inheritance

—

ClinVar variants

P:4U:11B:13

Top phenotype

CECR2-related neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr22:17,359,949-17,558,151

External References & Databases

Ensembl (ENSG00000099954)

Transcript & Mutation Effects

hg38 • Region Span ~198.2 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 CECR2 variants in ClinVar

3 Conditions Cataloged

not providedTotal: 18

CECR2-related neurodevelopmental disorderTotal: 6

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001290047.2. 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			3 clinvar	2 clinvar	6 clinvar	11
missense		1 clinvar	5 clinvar	2 clinvar	3 clinvar	11
nonsense		2 clinvar	1 clinvar			3
start loss						0
frameshift		1 clinvar	2 clinvar			3
splice donor/acceptor (+/-2bp)						0
Total	0	4	11	4	9	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001290047.2	RefSeq	NP_001276976.1	19	MANE Select
ENST00000262608.13	Ensembl	ENSP00000262608.11	19	MANE Select
NM_001290046.2	RefSeq	NP_001276975.1	16	Standard
ENST00000342247.10	Ensembl	ENSP00000341219.6	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic DNA fragmentation
cytoskeleton organization
vesicle-mediated transport
neural tube development
ATP-dependent chromatin remodeling

Cellular Component

nucleus
CERF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262608
Coding exons: 18
Length: 197014
Individuals with no LoFs: 124591
Homozygous LoFs: 0
Heterozygous LoFs: 105
Defined: 124696
p: 0.000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.573	801	848	0.945	0.0000494	9360
Missense (PolyPhen)		251	316.54	0.79295		3644
Synonymous	-1.40	360	328	1.10	0.0000203	2900
Loss of Function	7.14	6	70.9	0.0847	0.00000435	734

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00022	0.00019	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0041	0.0040	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000055	0.000053	rare
South Asian	0.00045	0.00042	rare
Other	0.00085	0.00083	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Chromatin reader component of histone-modifying complexes, such as the CERF (CECR2-containing-remodeling factor) complex and ISWI-type complex (PubMed:15640247, PubMed:26365797, PubMed:22464331). It thereby plays a role in various processes during development: required during embryogenesis for neural tube closure and inner ear development. In adults, required for spermatogenesis, via the formation of ISWI-type chromatin complexes (By similarity). In histone-modifying complexes, CECR2 recognizes and binds acylated histones: binds histones that are acetylated and/or butyrylated (PubMed:26365797, PubMed:22464331). May also be involved through its interaction with LRPPRC in the integration of cytoskeletal network with vesicular trafficking, nucleocytosolic shuttling, transcription, chromosome remodeling and cytokinesis (PubMed:11827465). {ECO:0000250|UniProtKB:E9Q2Z1, ECO:0000269|PubMed:11827465, ECO:0000269|PubMed:15640247, ECO:0000269|PubMed:22464331, ECO:0000269|PubMed:26365797}.;

Recessive Scores

pRec: 0.112

Essentials

Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.423

Gene Damage Prediction

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