CECR2

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

Basic information

Region (hg38): 22:17359948-17558151

Links

ENSG00000099954 ∙ NCBI:27443 ∙ OMIM:607576 ∙ HGNC:1840 ∙ Uniprot:Q9BXF3 ∙ 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 CECR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CECR2 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				2	6	8
missense				2	3	5
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	2	4	9

Variants in CECR2

This is a list of pathogenic ClinVar variants found in the CECR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-17511843-T-G			Benign (Dec 31, 2019)
22-17524110-C-T			Benign (Jun 21, 2018)
22-17537137-G-A			Likely benign (Jul 05, 2018)
22-17537213-G-GA			Uncertain significance (May 20, 2022)
22-17538986-C-T			Benign (Jul 05, 2018)
22-17540693-A-G			Benign (Dec 31, 2019)
22-17542187-C-A			Likely benign (Dec 31, 2019)
22-17542357-T-C			Benign (Dec 31, 2019)
22-17542371-C-T			Benign (Jun 10, 2018)
22-17542424-C-T		Autism;Global developmental delay;Abnormality of pain sensation;Aggressive behavior;Cleft lip	Uncertain significance (May 11, 2021)
22-17542684-C-T			Benign (Dec 31, 2019)
22-17542825-C-T			Likely benign (Apr 13, 2018)
22-17548287-A-G			Benign (Dec 31, 2019)
22-17548476-T-C			Benign (Dec 31, 2019)
22-17548949-G-A			Likely benign (Dec 31, 2019)
22-17549256-G-A			Benign (Jun 10, 2018)
22-17552064-G-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CECR2	protein_coding	protein_coding	ENST00000262608	18	197014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.10e-7	124591	0	105	124696	0.000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.573	801	848	0.945	0.0000494	9360
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000306	0.000280
Ashkenazi Jewish	0.00	0.00
East Asian	0.00414	0.00401
Finnish	0.000142	0.000139
European (Non-Finnish)	0.0000546	0.0000531
Middle Eastern	0.00414	0.00401
South Asian	0.000447	0.000425
Other	0.000854	0.000825

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.165
• ghis: 0.554

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.423

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cecr2
• Phenotype: immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: apoptotic DNA fragmentation;cytoskeleton organization;vesicle-mediated transport;neural tube development;ATP-dependent chromatin remodeling;cytoskeleton-dependent cytokinesis;execution phase of apoptosis
• Cellular component: nucleus;CERF complex