CSN3

casein kappa

Basic information

Region (hg38): 4:70238382-70251474

Previous symbols: [ "CSN10" ]

Links

ENSG00000171209 ∙ NCBI:1448 ∙ OMIM:601695 ∙ HGNC:2446 ∙ Uniprot:P07498 ∙ 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 CSN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSN3 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in CSN3

This is a list of pathogenic ClinVar variants found in the CSN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-70247845-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-70249054-G-A		not specified	Likely benign (Jul 12, 2023)
4-70249056-A-G		not specified	Uncertain significance (May 27, 2022)
4-70249064-C-T		not specified	Uncertain significance (Dec 03, 2021)
4-70249077-C-G		not specified	Uncertain significance (Dec 25, 2024)
4-70249098-A-T		not specified	Uncertain significance (Oct 12, 2022)
4-70249103-C-T		not specified	Uncertain significance (Jul 13, 2021)
4-70249109-C-A		not specified	Uncertain significance (Feb 12, 2025)
4-70249116-T-C		not specified	Uncertain significance (Mar 07, 2025)
4-70249128-A-G		not specified	Uncertain significance (Dec 15, 2022)
4-70249130-C-T		not specified	Uncertain significance (Dec 25, 2024)
4-70249143-G-A		not specified	Uncertain significance (Jul 26, 2024)
4-70249146-C-T		not specified	Uncertain significance (Aug 17, 2021)
4-70249174-G-T		not specified	Uncertain significance (Oct 30, 2023)
4-70249205-C-A		not specified	Uncertain significance (Jan 18, 2025)
4-70249236-G-A		not specified	Likely benign (Sep 27, 2024)
4-70249265-G-A		not specified	Uncertain significance (Jan 03, 2022)
4-70249295-A-G		not specified	Uncertain significance (Jun 26, 2023)
4-70249328-G-T		not specified	Uncertain significance (Dec 13, 2024)
4-70249361-A-G		not specified	Uncertain significance (Sep 26, 2022)
4-70249362-C-T		not specified	Uncertain significance (Oct 28, 2024)
4-70249407-T-C		not specified	Uncertain significance (Aug 21, 2024)
4-70249410-C-T		not specified	Uncertain significance (Jan 24, 2025)
4-70249419-C-G		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSN3	protein_coding	protein_coding	ENST00000304954	3	8841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0118	0.655	125586	0	3	125589	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0267	105	104	1.01	0.00000564	1155
Missense in Polyphen		3	4.278	0.70127		41
Synonymous	-0.859	44	37.3	1.18	0.00000185	384
Loss of Function	0.475	3	4.03	0.744	1.68e-7	57

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)	0.00000964	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000679	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Kappa-casein stabilizes micelle formation, preventing casein precipitation in milk.
• Pathway: Splicing factor NOVA regulated synaptic proteins (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.792
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.16

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.276

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0329

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csn3
• Phenotype: endocrine/exocrine gland 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)

Gene ontology

• Biological process: lactation;protein stabilization;transmembrane transport
• Cellular component: extracellular region;extracellular space
• Molecular function: molecular_function;protein binding