CAPZA3

capping actin protein of muscle Z-line subunit alpha 3, the group of Dynactin subunits

Basic information

Region (hg38): 12:18738119-18739188

Links

ENSG00000177938 ∙ NCBI:93661 ∙ OMIM:608722 ∙ HGNC:24205 ∙ Uniprot:Q96KX2 ∙ 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 CAPZA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPZA3 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in CAPZA3

This is a list of pathogenic ClinVar variants found in the CAPZA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-18738281-G-A		not specified	Uncertain significance (Oct 18, 2021)
12-18738289-C-A		not specified	Uncertain significance (Jan 30, 2024)
12-18738291-G-T		not specified	Uncertain significance (Dec 14, 2024)
12-18738357-C-G		not specified	Uncertain significance (May 26, 2023)
12-18738416-T-C		not specified	Uncertain significance (Apr 06, 2024)
12-18738503-G-A		not specified	Uncertain significance (Aug 28, 2024)
12-18738506-G-A		not specified	Uncertain significance (Jul 13, 2021)
12-18738524-C-G		not specified	Uncertain significance (Jul 20, 2021)
12-18738636-G-A		not specified	Uncertain significance (Mar 03, 2022)
12-18738638-G-A		not specified	Uncertain significance (Dec 15, 2023)
12-18738733-T-G		not specified	Uncertain significance (Feb 28, 2025)
12-18738743-A-C		not specified	Uncertain significance (Apr 08, 2024)
12-18738750-A-T		not specified	Uncertain significance (May 08, 2024)
12-18738753-C-A		not specified	Uncertain significance (Jan 08, 2024)
12-18738860-T-A		not specified	Uncertain significance (Jan 20, 2025)
12-18738876-T-C		not specified	Uncertain significance (Jul 13, 2021)
12-18738936-T-G		not specified	Uncertain significance (Mar 24, 2023)
12-18738944-G-T		not specified	Uncertain significance (Dec 16, 2022)
12-18738953-G-A		not specified	Uncertain significance (Jul 19, 2022)
12-18738970-C-A		not specified	Uncertain significance (Sep 20, 2024)
12-18738987-T-C		not specified	Uncertain significance (Jun 16, 2023)
12-18739010-T-C		not specified	Uncertain significance (Jan 03, 2025)
12-18739038-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-18739042-G-C		not specified	Uncertain significance (Aug 21, 2023)
12-18739059-G-T		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPZA3	protein_coding	protein_coding	ENST00000317658	1	1077

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000971	0.825	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.257	164	155	1.06	0.00000753	1980
Missense in Polyphen		53	52.902	1.0018		705
Synonymous	-0.799	67	59.2	1.13	0.00000306	554
Loss of Function	1.17	6	9.97	0.602	6.06e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: F-actin-capping proteins bind in a Ca(2+)-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike other capping proteins (such as gelsolin and severin), these proteins do not sever actin filaments. May play a role in the morphogenesis of spermatid (By similarity). {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0999

Intolerance Scores

• loftool: 0.237
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.248

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capza3
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;spermatid development;antigen processing and presentation of exogenous peptide antigen via MHC class II;actin cytoskeleton organization;barbed-end actin filament capping
• Cellular component: acrosomal vesicle;nucleus;cytosol;F-actin capping protein complex;membrane;actin cortical patch
• Molecular function: actin filament binding