CHN2

chimerin 2, the group of Rho GTPase activating proteins|SH2 domain containing

Basic information

Region (hg38): 7:29146547-29514328

Links

ENSG00000106069 ∙ NCBI:1124 ∙ OMIM:602857 ∙ HGNC:1944 ∙ Uniprot:P52757 ∙ 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 CHN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHN2 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	2	4
missense			15	2	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1	1	2
Total	0	0	16	5	4

Variants in CHN2

This is a list of pathogenic ClinVar variants found in the CHN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-29146601-G-A		CHN2-related disorder	Benign (Oct 22, 2019)
7-29146646-C-T		CHN2-related disorder	Likely benign (Feb 21, 2022)
7-29146736-T-G		CHN2-related disorder	Benign (Aug 10, 2019)
7-29146841-C-T		CHN2-related disorder	Benign (Oct 28, 2019)
7-29146908-T-C		CHN2-related disorder	Likely benign (Jan 20, 2020)
7-29194936-G-A		CHN2-related disorder	Likely benign (May 17, 2019)
7-29194958-A-C		not specified	Uncertain significance (May 09, 2023)
7-29263959-CGTCTGGGAGGTGGGGGGGCAGCCCCCGCCCAGCCAGCCGCCCCA-C		Schizophrenia	Uncertain significance (Nov 11, 2022)
7-29292923-A-T		CHN2-related disorder	Benign (Jun 07, 2019)
7-29354660-T-A		not specified	Uncertain significance (May 24, 2024)
7-29360106-AACCCCACAGGTTTCTCTTATACATACTTACGCCTGAAAC-A		Schizophrenia	Uncertain significance (Nov 11, 2022)
7-29367934-T-C			Likely benign (Apr 04, 2024)
7-29398455-C-T		not specified	Uncertain significance (Aug 16, 2022)
7-29400536-C-T		CHN2-related disorder	Benign (Feb 22, 2019)
7-29400658-A-G		not specified	Uncertain significance (Jul 15, 2021)
7-29400697-A-G		not specified	Uncertain significance (Nov 21, 2023)
7-29400724-T-ATCC		CHN2-related disorder	Uncertain significance (Dec 31, 2023)
7-29400749-T-C		not specified	Uncertain significance (Nov 18, 2022)
7-29496012-A-G		not specified	Uncertain significance (May 14, 2024)
7-29499961-C-T		CHN2-related disorder	Benign (Jun 13, 2019)
7-29499997-A-C		not specified	Uncertain significance (Jul 17, 2023)
7-29500023-G-A		not specified	Uncertain significance (Dec 06, 2022)
7-29504721-GTCTC-G		CHN2-related disorder	Likely benign (Aug 24, 2023)
7-29504792-T-A		not specified	Uncertain significance (Jul 19, 2023)
7-29507241-C-T		CHN2-related disorder	Likely benign (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHN2	protein_coding	protein_coding	ENST00000222792	13	392055

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00230	0.997	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	214	266	0.805	0.0000144	3072
Missense in Polyphen		97	141.33	0.68632		1577
Synonymous	1.11	89	103	0.862	0.00000615	872
Loss of Function	2.97	9	25.0	0.360	0.00000120	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000583	0.0000583
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000277	0.000277
European (Non-Finnish)	0.0000369	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000208	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein for p21-rac. Insufficient expression of beta-2 chimaerin is expected to lead to higher Rac activity and could therefore play a role in the progression from low-grade to high-grade tumors.
• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;Regulation of RAC1 activity;ErbB1 downstream signaling (Consensus)

Intolerance Scores

• loftool: 0.454
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.694
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.762

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chn2
• 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); cellular phenotype

Gene ontology

• Biological process: positive regulation of signal transduction;intracellular signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol;membrane
• Molecular function: SH3/SH2 adaptor activity;GTPase activator activity;protein binding;metal ion binding