CASKIN1

CASK interacting protein 1, the group of Ankyrin repeat domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 16:2177180-2196605

Links

ENSG00000167971 ∙ NCBI:57524 ∙ OMIM:612184 ∙ HGNC:20879 ∙ Uniprot:Q8WXD9 ∙ 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 CASKIN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASKIN1 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				3		3
missense			106	3		109
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	106	6	0

Variants in CASKIN1

This is a list of pathogenic ClinVar variants found in the CASKIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2178555-C-G		not specified	Uncertain significance (Jan 30, 2024)
16-2178621-C-T		not specified	Uncertain significance (Aug 02, 2022)
16-2178641-G-A		not specified	Uncertain significance (Nov 22, 2022)
16-2178903-G-A		not specified	Uncertain significance (May 18, 2022)
16-2178917-T-A		not specified	Uncertain significance (Oct 21, 2021)
16-2179002-C-A		not specified	Uncertain significance (Jan 27, 2022)
16-2179005-C-T		not specified	Uncertain significance (Aug 30, 2021)
16-2179083-C-T		not specified	Uncertain significance (Feb 16, 2023)
16-2179116-G-A		not specified	Uncertain significance (Dec 14, 2021)
16-2179146-G-A		not specified	Uncertain significance (Jan 26, 2023)
16-2179149-G-A		not specified	Uncertain significance (Feb 14, 2023)
16-2179155-C-T		not specified	Likely benign (Nov 12, 2021)
16-2179160-G-A		not specified	Uncertain significance (May 28, 2024)
16-2179179-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-2179181-G-A		not specified	Uncertain significance (Nov 13, 2023)
16-2179202-G-A		not specified	Uncertain significance (Jan 03, 2024)
16-2179254-G-A		not specified	Uncertain significance (Mar 20, 2024)
16-2179289-G-A		not specified	Uncertain significance (Dec 27, 2023)
16-2179317-G-C		not specified	Uncertain significance (Jun 22, 2023)
16-2179641-G-A		not specified	Uncertain significance (Aug 30, 2022)
16-2179662-C-T		not specified	Likely benign (Jul 13, 2022)
16-2179788-G-C		not specified	Uncertain significance (Oct 05, 2021)
16-2179811-G-T		not specified	Uncertain significance (Nov 16, 2021)
16-2179835-C-T		not specified	Uncertain significance (Dec 21, 2022)
16-2179873-C-T			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASKIN1	protein_coding	protein_coding	ENST00000343516	20	19343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000499	124596	0	8	124604	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	665	808	0.823	0.0000557	8895
Missense in Polyphen		231	350.88	0.65835		3558
Synonymous	-2.53	455	391	1.16	0.0000316	3156
Loss of Function	5.98	3	47.4	0.0633	0.00000265	550

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000302	0.0000302
Ashkenazi Jewish	0.0000997	0.0000995
East Asian	0.0000560	0.0000556
Finnish	0.0000641	0.0000464
European (Non-Finnish)	0.0000289	0.0000266
Middle Eastern	0.0000560	0.0000556
South Asian	0.00	0.00
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May link the scaffolding protein CASK to downstream intracellular effectors. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.236
• hipred: Y
• hipred_score: 0.806
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Caskin1
• Phenotype: homeostasis/metabolism 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); endocrine/exocrine gland phenotype; pigmentation phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: signal transduction
• Cellular component: cytoplasm;membrane
• Molecular function: protein binding;identical protein binding