CSN2

casein beta

Basic information

Region (hg38): 4:69955256-69965728

Previous symbols: [ "CASB" ]

Links

ENSG00000135222 ∙ NCBI:1447 ∙ OMIM:115460 ∙ HGNC:2447 ∙ Uniprot:P05814 ∙ 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 CSN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSN2 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				1		1
missense			19	7		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	8	0

Variants in CSN2

This is a list of pathogenic ClinVar variants found in the CSN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-69957275-C-G		not specified	Uncertain significance (Jul 16, 2021)
4-69957288-G-A		not specified	Likely benign (Aug 21, 2023)
4-69957308-G-C		not specified	Uncertain significance (Oct 30, 2024)
4-69957342-G-T		not specified	Uncertain significance (Feb 15, 2023)
4-69957368-T-C		not specified	Uncertain significance (Jan 26, 2022)
4-69957411-G-A		not specified	Uncertain significance (Dec 15, 2023)
4-69957444-A-G		not specified	Uncertain significance (Mar 20, 2024)
4-69957450-G-A		not specified	Likely benign (Jun 24, 2022)
4-69957465-C-T		not specified	Uncertain significance (Mar 20, 2024)
4-69957477-G-A		not specified	Uncertain significance (Apr 08, 2024)
4-69957525-G-A		not specified	Uncertain significance (Aug 28, 2024)
4-69957571-A-T		not specified	Likely benign (Jul 19, 2022)
4-69957572-A-G		not specified	Uncertain significance (Feb 21, 2024)
4-69957584-G-A		not specified	Likely benign (Apr 18, 2023)
4-69957584-G-C		not specified	Uncertain significance (Aug 30, 2021)
4-69957672-C-A		not specified	Likely benign (Aug 30, 2022)
4-69957690-G-T		not specified	Uncertain significance (Jul 10, 2023)
4-69957732-G-T		not specified	Uncertain significance (Dec 21, 2023)
4-69957752-T-G		not specified	Uncertain significance (Jun 18, 2024)
4-69957755-A-T		not specified	Uncertain significance (Oct 04, 2024)
4-69957784-G-C		not specified	Uncertain significance (Jun 27, 2023)
4-69957785-A-G		not specified	Uncertain significance (Dec 12, 2023)
4-69957796-G-A			Likely benign (Feb 01, 2023)
4-69957797-T-C		not specified	Likely benign (Jan 18, 2022)
4-69958938-C-A		not specified	Likely benign (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSN2	protein_coding	protein_coding	ENST00000353151	6	5752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000718	0.504	125472	0	5	125477	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.47	158	114	1.39	0.00000516	1449
Missense in Polyphen		35	22.008	1.5903		272
Synonymous	-2.41	62	42.1	1.47	0.00000202	470
Loss of Function	0.659	9	11.4	0.789	4.88e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000637	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important role in determination of the surface properties of the casein micelles.
• Pathway: Prolactin signaling pathway - Homo sapiens (human);Signaling by ERBB4;Signal Transduction;Glucocorticoid receptor regulatory network;Nuclear signaling by ERBB4;Signaling by ERBB4;Signaling by Receptor Tyrosine Kinases;Signaling events mediated by PTP1B (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.319
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.0778
• 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: 0.0477

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csn2
• 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: calcium ion transport;lactation;negative regulation of lactation;negative regulation of cysteine-type endopeptidase activity
• Cellular component: extracellular region;extracellular space
• Molecular function: enzyme inhibitor activity;cysteine-type endopeptidase inhibitor activity;calcium ion binding