CABS1

calcium binding protein, spermatid associated 1

Basic information

Region (hg38): 4:70334980-70337116

Previous symbols: [ "C4orf35" ]

Links

ENSG00000145309 ∙ NCBI:85438 ∙ OMIM:618600 ∙ HGNC:30710 ∙ Uniprot:Q96KC9 ∙ 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 CABS1 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CABS1 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			10	2	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	1

Variants in CABS1

This is a list of pathogenic ClinVar variants found in the CABS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-70335053-G-A		not specified	Uncertain significance (Dec 06, 2021)
4-70335082-A-G			Benign (Oct 19, 2017)
4-70335239-A-C		not specified	Uncertain significance (Sep 26, 2023)
4-70335266-A-G		not specified	Likely benign (Sep 29, 2023)
4-70335385-A-G		not specified	Uncertain significance (Sep 07, 2022)
4-70335463-G-A		not specified	Uncertain significance (May 11, 2022)
4-70335515-C-T		not specified	Uncertain significance (Feb 02, 2024)
4-70335580-C-G		not specified	Uncertain significance (Mar 08, 2024)
4-70335649-G-T		not specified	Uncertain significance (Mar 29, 2022)
4-70335659-T-C		not specified	Uncertain significance (Jun 23, 2023)
4-70335770-T-C		not specified	Uncertain significance (Dec 31, 2023)
4-70335881-G-A		not specified	Likely benign (Aug 17, 2022)
4-70335902-A-G		not specified	Uncertain significance (Dec 08, 2023)
4-70335923-C-A		not specified	Uncertain significance (Oct 10, 2023)
4-70335928-A-G		not specified	Likely benign (Jan 23, 2024)
4-70335946-A-G		not specified	Uncertain significance (Jun 06, 2023)
4-70335965-C-T		not specified	Uncertain significance (Apr 18, 2023)
4-70336090-A-T		not specified	Likely benign (Jan 26, 2022)
4-70336112-C-T		not specified	Uncertain significance (Jun 24, 2022)
4-70336132-G-C		not specified	Uncertain significance (Jul 26, 2022)
4-70336181-A-G		not specified	Likely benign (Jan 24, 2024)
4-70336203-A-C		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CABS1	protein_coding	protein_coding	ENST00000273936	1	2151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00763	0.793	125600	0	57	125657	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.480	223	204	1.09	0.00000966	2585
Missense in Polyphen		43	41.275	1.0418		519
Synonymous	-0.792	88	79.0	1.11	0.00000430	814
Loss of Function	0.987	4	6.77	0.591	2.79e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000396	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000196	0.000194
Middle Eastern	0.00	0.00
South Asian	0.000523	0.000523
Other	0.000822	0.000816

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cabs1

Gene ontology

• Biological process: spermatogenesis
• Cellular component: mitochondrial inner membrane;motile cilium
• Molecular function: calcium ion binding