CNIH4

cornichon family AMPA receptor auxiliary protein 4

Basic information

Region (hg38): 1:224356858-224379459

Links

ENSG00000143771 ∙ NCBI:29097 ∙ OMIM:617483 ∙ HGNC:25013 ∙ Uniprot:Q9P003 ∙ 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 CNIH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNIH4 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in CNIH4

This is a list of pathogenic ClinVar variants found in the CNIH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-224356931-G-T		not specified	Uncertain significance (Dec 10, 2024)
1-224356932-C-G		not specified	Uncertain significance (Oct 18, 2021)
1-224356938-T-A		not specified	Uncertain significance (Jan 10, 2025)
1-224356943-G-C		not specified	Uncertain significance (May 26, 2022)
1-224356952-C-T		not specified	Uncertain significance (Nov 27, 2024)
1-224356983-C-T		not specified	Uncertain significance (May 01, 2022)
1-224371379-C-G		not specified	Uncertain significance (Oct 20, 2024)
1-224371412-G-C		not specified	Uncertain significance (Apr 24, 2024)
1-224375802-T-G		not specified	Uncertain significance (Dec 16, 2024)
1-224375817-G-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNIH4	protein_coding	protein_coding	ENST00000465271	5	22610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0217	0.915	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.231	68	73.6	0.924	0.00000338	914
Missense in Polyphen		22	23.121	0.95153		329
Synonymous	-0.734	31	26.2	1.18	0.00000121	244
Loss of Function	1.59	4	9.18	0.436	5.20e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000333	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in G protein-coupled receptors (GPCRs) trafficking from the endoplasmic reticulum to the cell surface; it promotes the exit of GPCRs from the early secretory pathway, likely through interaction with the COPII machinery (PubMed:24405750). {ECO:0000269|PubMed:24405750}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.688
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.734
• hipred: N
• hipred_score: 0.370
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.821

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnih4

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;protein transport
• Cellular component: endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;integral component of membrane
• Molecular function: protein binding;CCR5 chemokine receptor binding