CHIC1

protein-coding

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

Gene summary

This gene encodes a cysteine-rich hydrophobic (CHIC) domain-containing protein, and is one of the few protein-coding genes found near the X-inactivation center. Studies in mouse indicate that the mouse ortholog of this gene is subject to X-inactivation in mouse. Experiments with other CHIC domain-containing family members show that the cysteine residues are palmitoylated post-translationally, resulting in membrane association. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2017]

MANE transcript

NM_001039840.4

Inheritance

—

ClinVar variants

U:55

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:73,563,197-73,687,111

External References & Databases

Ensembl (ENSG00000204116)

Transcript & Mutation Effects

hg38 • Region Span ~123.9 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 CHIC1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 25

not providedTotal: 2

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001039840.4. 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			4 clinvar			4
missense			42 clinvar			42
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	55	0	0	55

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001039840.4	RefSeq	NP_001034929.2	6	MANE Select
ENST00000373502.10	Ensembl	ENSP00000362601.5	6	MANE Select
NM_001300884.1	RefSeq	NP_001287813.1	5	Standard
ENST00000373504.10	Ensembl	ENSP00000362603.5	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

plasma membrane
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373502
Coding exons: 6
Length: 123902
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.588	48	60.9	0.788	0.00000421	1438
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

RVIS EVS: 0.06
RVIS percentile EVS: 58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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