CASS4

Cas scaffold protein family member 4, the group of Cas scaffold proteins

Basic information

Region (hg38): 20:56412111-56460387

Previous symbols: [ "C20orf32" ]

Links

ENSG00000087589 ∙ NCBI:57091 ∙ OMIM:618888 ∙ HGNC:15878 ∙ Uniprot:Q9NQ75 ∙ 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 CASS4 gene.

• Inborn genetic diseases (32 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CASS4 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	2
missense			25	9	2	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	10	3

Variants in CASS4

This is a list of pathogenic ClinVar variants found in the CASS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-56412474-A-G		not specified	Likely benign (Jul 26, 2022)
20-56437174-C-A		not specified	Uncertain significance (Feb 17, 2022)
20-56437245-A-G		not specified	Uncertain significance (Aug 14, 2023)
20-56437327-G-A		not specified	Uncertain significance (Mar 07, 2023)
20-56437340-C-T			Benign (Mar 29, 2018)
20-56437372-C-A		not specified	Uncertain significance (Feb 17, 2022)
20-56437440-C-T		not specified	Likely benign (Aug 22, 2023)
20-56437480-G-A		not specified	Uncertain significance (Mar 01, 2024)
20-56445990-G-A		not specified	Uncertain significance (Apr 05, 2023)
20-56450663-C-G		not specified	Uncertain significance (Sep 29, 2022)
20-56451838-T-C		not specified	Likely benign (Jan 23, 2023)
20-56451885-C-A		not specified	Uncertain significance (Aug 02, 2023)
20-56451913-C-T		not specified	Uncertain significance (May 10, 2022)
20-56451939-G-A		not specified	Likely benign (Oct 28, 2023)
20-56451949-C-T		not specified	Uncertain significance (Jan 05, 2022)
20-56451967-C-T		not specified	Likely benign (Mar 21, 2023)
20-56451973-A-C		not specified	Uncertain significance (Oct 25, 2022)
20-56452002-A-G		not specified	Likely benign (Nov 07, 2022)
20-56452008-A-G		not specified	Uncertain significance (May 06, 2022)
20-56452018-A-G		not specified	Likely benign (Oct 02, 2023)
20-56452059-A-T		not specified	Uncertain significance (Feb 28, 2024)
20-56452243-C-T		not specified	Likely benign (Apr 07, 2022)
20-56452305-G-A		not specified	Likely benign (Mar 17, 2023)
20-56452408-C-G			Likely benign (Mar 29, 2018)
20-56452450-C-T		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CASS4	protein_coding	protein_coding	ENST00000371336	6	47229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.367	0.633	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	392	459	0.853	0.0000264	5120
Missense in Polyphen		73	107.29	0.68038		1295
Synonymous	-0.143	193	190	1.01	0.0000120	1604
Loss of Function	3.70	6	26.5	0.226	0.00000138	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000452	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.000295	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Docking protein that plays a role in tyrosine kinase- based signaling related to cell adhesion and cell spreading. Regulates PTK2/FAK1 activity, focal adhesion integrity, and cell spreading. {ECO:0000269|PubMed:18256281}.

Recessive Scores

• pRec: 0.0839

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.65

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.403
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.314

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cass4

Gene ontology

• Biological process: cell adhesion;cell migration;positive regulation of cell migration;positive regulation of protein tyrosine kinase activity;actin filament reorganization;positive regulation of substrate adhesion-dependent cell spreading
• Cellular component: cytoplasm;cytoskeleton;plasma membrane;focal adhesion
• Molecular function: protein tyrosine kinase binding