CHIC1

cysteine rich hydrophobic domain 1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): X:73563197-73687111

Links

ENSG00000204116 ∙ NCBI:53344 ∙ OMIM:300922 ∙ HGNC:1934 ∙ Uniprot:Q5VXU3 ∙ 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 CHIC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHIC1 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in CHIC1

This is a list of pathogenic ClinVar variants found in the CHIC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-73563355-A-C		not specified	Uncertain significance (Aug 05, 2024)
X-73563417-G-A		not specified	Uncertain significance (Jul 25, 2023)
X-73563433-A-G		not specified	Uncertain significance (Jan 30, 2024)
X-73563434-AGAGGAGGAAGAGGAG-A			Uncertain significance (Jun 01, 2022)
X-73563439-A-C		not specified	Uncertain significance (Mar 14, 2023)
X-73563448-A-G		not specified	Uncertain significance (Feb 22, 2023)
X-73563504-C-T		not specified	Uncertain significance (Feb 25, 2025)
X-73563515-C-G		not specified	Uncertain significance (Mar 21, 2023)
X-73563521-G-C		not specified	Uncertain significance (Jul 31, 2024)
X-73563540-C-G		not specified	Uncertain significance (Jan 02, 2024)
X-73563540-C-T		not specified	Uncertain significance (May 24, 2023)
X-73577441-C-T		Prostate cancer	Uncertain significance (-)
X-73577447-G-A		not specified	Uncertain significance (Mar 14, 2023)
X-73584462-T-A		not specified	Uncertain significance (Jul 25, 2023)
X-73584481-C-T		not specified	Uncertain significance (Nov 14, 2024)
X-73679327-C-G		not specified	Uncertain significance (Oct 29, 2024)
X-73680960-A-G		not specified	Uncertain significance (Jan 18, 2025)
X-73680973-T-G		not specified	Uncertain significance (Feb 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHIC1	protein_coding	protein_coding	ENST00000373502	6	123902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.853	0.145	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.588	48	60.9	0.788	0.00000421	1438
Missense in Polyphen		9	22.576	0.39865		525
Synonymous	-1.15	32	24.7	1.29	0.00000185	391
Loss of Function	2.32	0	6.28	0.00	3.98e-7	165

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.372
• hipred: Y
• hipred_score: 0.579
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chic1
• Phenotype: normal phenotype

Gene ontology

• Cellular component: plasma membrane;cytoplasmic vesicle