CAPSL

calcyphosine like, the group of EF-hand domain containing

Basic information

Region (hg38): 5:35904288-35938779

Links

ENSG00000152611 ∙ NCBI:133690 ∙ OMIM:618799 ∙ HGNC:28375 ∙ Uniprot:Q8WWF8 ∙ 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 CAPSL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPSL 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			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	1

Variants in CAPSL

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

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

Position	Type	Phenotype	Significance	ClinVar
5-35904554-C-G		not specified	Uncertain significance (Nov 17, 2022)
5-35904571-T-C			Benign (Jun 18, 2018)
5-35904577-T-C		not specified	Uncertain significance (Feb 14, 2023)
5-35904582-T-C		not specified	Uncertain significance (Feb 23, 2023)
5-35904586-C-T		not specified	Uncertain significance (Jan 23, 2024)
5-35904597-A-G		not specified	Uncertain significance (Dec 12, 2023)
5-35904605-G-T		not specified	Uncertain significance (Aug 12, 2021)
5-35904643-T-A		not specified	Uncertain significance (Nov 30, 2022)
5-35909940-C-T		not specified	Uncertain significance (Aug 13, 2021)
5-35909961-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-35910067-C-A		not specified	Uncertain significance (Oct 06, 2023)
5-35910413-C-A		not specified	Uncertain significance (Oct 12, 2021)
5-35910443-C-T		not specified	Uncertain significance (Dec 16, 2023)
5-35910456-C-T		not specified	Uncertain significance (Aug 16, 2022)
5-35910481-C-T		Autism	Uncertain significance (-)
5-35910500-A-C		not specified	Uncertain significance (Feb 10, 2023)
5-35910502-T-G		not specified	Uncertain significance (Oct 05, 2021)
5-35920994-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-35921025-C-G		not specified	Uncertain significance (May 05, 2023)
5-35921059-G-A		not specified	Uncertain significance (May 30, 2023)
5-35921063-T-A		not specified	Uncertain significance (Jun 24, 2022)
5-35921093-C-G		not specified	Uncertain significance (Apr 04, 2023)
5-35921117-C-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPSL	protein_coding	protein_coding	ENST00000397367	4	34485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.84e-7	0.178	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.491	134	119	1.13	0.00000625	1387
Missense in Polyphen		50	35.528	1.4074		441
Synonymous	-1.43	55	43.1	1.28	0.00000248	367
Loss of Function	-0.0126	10	9.96	1.00	6.56e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000462	0.000458
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.000996	0.000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.470
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.397
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capsl

Gene ontology

• Cellular component: cytoplasm
• Molecular function: calcium ion binding