CSN1S1

casein alpha s1

Basic information

Region (hg38): 4:69931068-69946574

Previous symbols: [ "CASA", "CSN1" ]

Links

ENSG00000126545 ∙ NCBI:1446 ∙ OMIM:115450 ∙ HGNC:2445 ∙ Uniprot:P47710 ∙ 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 CSN1S1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSN1S1 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	12	1	0

Variants in CSN1S1

This is a list of pathogenic ClinVar variants found in the CSN1S1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-69932596-T-C		not specified	Uncertain significance (Nov 19, 2024)
4-69934236-C-T		not specified	Uncertain significance (Nov 23, 2022)
4-69934249-A-G			Benign (Jul 31, 2018)
4-69934693-C-T		not specified	Uncertain significance (Oct 05, 2023)
4-69934701-G-C		not specified	Likely benign (Nov 06, 2023)
4-69935922-G-T			Likely benign (Jan 08, 2018)
4-69937124-A-G		not specified	Uncertain significance (Jun 11, 2021)
4-69939181-G-A		not specified	Uncertain significance (Jan 02, 2024)
4-69939191-A-G		not specified	Uncertain significance (Apr 07, 2022)
4-69944911-T-A		not specified	Uncertain significance (Mar 29, 2023)
4-69944943-G-A		not specified	Uncertain significance (Dec 12, 2023)
4-69944943-G-T		not specified	Uncertain significance (Aug 09, 2021)
4-69944976-G-C		not specified	Uncertain significance (Sep 09, 2021)
4-69944988-G-A		not specified	Uncertain significance (Jul 27, 2021)
4-69944991-A-G		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSN1S1	protein_coding	protein_coding	ENST00000246891	14	15491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-16	0.00166	124472	0	50	124522	0.000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.319	80	88.5	0.904	0.00000432	1207
Missense in Polyphen		12	14.338	0.83692		165
Synonymous	0.145	28	29.0	0.966	0.00000160	291
Loss of Function	-0.850	22	18.1	1.22	7.69e-7	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.0000996	0.0000994
East Asian	0.000228	0.000223
Finnish	0.000149	0.000139
European (Non-Finnish)	0.000388	0.000336
Middle Eastern	0.000228	0.000223
South Asian	0.0000682	0.0000654
Other	0.000184	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important role in the capacity of milk to transport calcium phosphate.

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.86

Haploinsufficiency Scores

• pHI: 0.0737
• hipred: N
• hipred_score: 0.228

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0427

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csn1s1
• 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: response to estradiol;response to progesterone;transmembrane transport;response to dehydroepiandrosterone;response to 11-deoxycorticosterone
• Cellular component: extracellular region;extracellular space