CASKIN2

CASK interacting protein 2, the group of Sterile alpha motif domain containing|Ankyrin repeat domain containing

Basic information

Region (hg38): 17:75500261-75515537

Links

ENSG00000177303 ∙ NCBI:57513 ∙ OMIM:612185 ∙ HGNC:18200 ∙ Uniprot:Q8WXE0 ∙ 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 CASKIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASKIN2 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			155	1		156
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	155	1	0

Variants in CASKIN2

This is a list of pathogenic ClinVar variants found in the CASKIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75501094-C-A		not specified	Uncertain significance (Aug 22, 2022)
17-75501118-C-T		not specified	Uncertain significance (Dec 16, 2024)
17-75501124-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-75501139-C-T		not specified	Uncertain significance (Nov 25, 2024)
17-75501148-G-A		not specified	Uncertain significance (Jan 09, 2024)
17-75501160-C-T		not specified	Likely benign (May 14, 2024)
17-75501616-C-T		not specified	Uncertain significance (Feb 07, 2025)
17-75501622-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-75501627-G-A		not specified	Uncertain significance (Aug 12, 2022)
17-75501639-C-T		not specified	Uncertain significance (Oct 25, 2024)
17-75501669-G-A		not specified	Uncertain significance (May 11, 2022)
17-75501788-G-A		not specified	Uncertain significance (Jul 13, 2021)
17-75501812-C-T		not specified	Uncertain significance (Apr 22, 2024)
17-75501814-G-A		not specified	Uncertain significance (Apr 12, 2022)
17-75501814-G-C		not specified	Uncertain significance (Sep 22, 2023)
17-75501817-G-A		not specified	Uncertain significance (Jan 07, 2022)
17-75501862-A-G		not specified	Uncertain significance (Jul 02, 2024)
17-75501883-G-A		not specified	Uncertain significance (Nov 17, 2023)
17-75501905-G-A		not specified	Uncertain significance (Dec 20, 2023)
17-75501956-C-T		not specified	Uncertain significance (Aug 01, 2022)
17-75501983-G-A		not specified	Uncertain significance (Nov 14, 2023)
17-75501991-C-G		not specified	Uncertain significance (Nov 07, 2024)
17-75501995-G-A		not specified	Uncertain significance (Jun 06, 2022)
17-75501995-G-C		not specified	Uncertain significance (Oct 20, 2023)
17-75501997-G-A		not specified	Uncertain significance (Apr 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASKIN2	protein_coding	protein_coding	ENST00000321617	19	15323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000292	125622	0	12	125634	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	682	738	0.924	0.0000483	7514
Missense in Polyphen		275	356.83	0.77067		3592
Synonymous	-0.973	347	325	1.07	0.0000223	2685
Loss of Function	5.55	5	45.4	0.110	0.00000217	512

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000110	0.0000905
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.00	0.00
Finnish	0.0000474	0.0000462
European (Non-Finnish)	0.0000672	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000668	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: TCR;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.0453
• rvis_EVS: -0.52
• rvis_percentile_EVS: 20.97

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.570
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.484

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Caskin2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: cytoplasm;membrane
• Molecular function: molecular_function