CHIC2

cysteine rich hydrophobic domain 2

Basic information

Region (hg38): 4:53994803-54064605

Links

ENSG00000109220

∙ NCBI:26511 ∙ OMIM:604332 ∙ HGNC:1935 ∙ Uniprot:Q9UKJ5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

acute myeloid leukemia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CHIC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHIC2 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						0
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	4	0	0

Variants in CHIC2

This is a list of pathogenic ClinVar variants found in the CHIC2 region.

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

Position	Phenotype	Significance	ClinVar
4-54010140-G-C	not specified	Uncertain significance (Oct 03, 2022)	3144356
4-54013896-G-A	not specified	Likely benign (May 22, 2023)	2568516
4-54048959-T-C	not specified	Uncertain significance (May 31, 2023)	2515174
4-54049115-A-G	CHIC2-related disorder	Likely benign (Mar 14, 2019)	3034507
4-54064242-T-G	not specified	Uncertain significance (Sep 06, 2022)	2310169
4-54064254-C-T	not specified	Uncertain significance (Mar 04, 2024)	3144357

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHIC2	protein_coding	protein_coding	ENST00000263921	6	54902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.542	0.455	125554	0	3	125557	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	48	86.6	0.554	0.00000428	1079
Missense in Polyphen		9	34.174	0.26336		449
Synonymous	0.241	31	32.8	0.947	0.00000169	280
Loss of Function	2.49	2	10.8	0.184	5.57e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.00000882	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Disease: DISEASE: Note=A chromosomal aberration involving CHIC2 is found in a form of acute myeloid leukemia (AML). Translocation t(4;12)(q12;p13) with ETV6. {ECO:0000269|PubMed:10477709}.;

Recessive Scores

pRec: 0.171

Intolerance Scores

loftool: 0.186
rvis_EVS: -0.16
rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

pHI: 0.734
hipred: Y
hipred_score: 0.528
ghis: 0.613

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Chic2
Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); reproductive system phenotype; pigmentation phenotype; vision/eye phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype;

Gene ontology

Biological process: biological_process
Cellular component: cellular_component;Golgi apparatus;Golgi-associated vesicle;plasma membrane;intracellular membrane-bounded organelle
Molecular function: molecular_function;protein binding