ZYX

zyxin, the group of MicroRNA protein coding host genes|Zyxin family

Basic information

Region (hg38): 7:143381295-143391111

Links

ENSG00000159840 ∙ NCBI:7791 ∙ OMIM:602002 ∙ HGNC:13200 ∙ Uniprot:Q15942 ∙ 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 ZYX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZYX 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				4	3	7
missense			38	4	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	8	4

Variants in ZYX

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

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

Position	Type	Phenotype	Significance	ClinVar
7-143381591-C-T		not specified	Uncertain significance (Jul 17, 2023)
7-143381722-G-A		not specified	Uncertain significance (Jan 02, 2024)
7-143381723-G-A		not specified	Uncertain significance (Nov 10, 2021)
7-143381728-C-A		not specified	Uncertain significance (Jun 05, 2024)
7-143381759-T-G			Benign (May 21, 2018)
7-143381763-C-T			Likely benign (Aug 01, 2022)
7-143382269-C-T		not specified	Uncertain significance (Dec 06, 2023)
7-143382315-C-T			Likely benign (Aug 01, 2023)
7-143382337-A-C		not specified	Uncertain significance (Dec 20, 2021)
7-143382362-C-T		not specified	Uncertain significance (Nov 07, 2023)
7-143382376-A-C		not specified	Uncertain significance (Jul 15, 2021)
7-143382400-C-T		not specified	Uncertain significance (Oct 02, 2023)
7-143382408-G-A			Likely benign (Aug 01, 2022)
7-143382413-G-A		not specified	Uncertain significance (Jan 16, 2024)
7-143382636-T-C		not specified	Uncertain significance (Mar 28, 2023)
7-143382829-T-G		not specified	Uncertain significance (Aug 09, 2021)
7-143382877-G-A			Likely benign (May 18, 2018)
7-143382937-C-T		not specified	Uncertain significance (Dec 30, 2023)
7-143382963-T-C		not specified	Uncertain significance (Aug 02, 2023)
7-143382988-C-T		not specified	Uncertain significance (Feb 27, 2024)
7-143383008-C-T		not specified	Uncertain significance (Oct 17, 2023)
7-143383009-A-T		not specified	Uncertain significance (Feb 22, 2023)
7-143383013-C-T			Likely benign (Mar 01, 2022)
7-143383039-T-C		not specified	Likely benign (May 05, 2023)
7-143383077-C-T		not specified	Uncertain significance (Jan 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZYX	protein_coding	protein_coding	ENST00000322764	9	10032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.03e-10	0.645	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.181	354	345	1.03	0.0000193	3652
Missense in Polyphen		98	111.05	0.88245		1174
Synonymous	0.718	141	152	0.926	0.00000944	1220
Loss of Function	1.40	19	26.8	0.708	0.00000158	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.000166	0.000163
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adhesion plaque protein. Binds alpha-actinin and the CRP protein. Important for targeting TES and ENA/VASP family members to focal adhesions and for the formation of actin-rich structures. May be a component of a signal transduction pathway that mediates adhesion-stimulated changes in gene expression (By similarity). {ECO:0000250}.
• Pathway: Focal adhesion - Homo sapiens (human);Integrin-mediated Cell Adhesion;Focal Adhesion;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;integrin signaling pathway;E-cadherin signaling in keratinocytes;Integrin-linked kinase signaling;Stabilization and expansion of the E-cadherin adherens junction;PAR1-mediated thrombin signaling events (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.314
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.98

Haploinsufficiency Scores

• pHI: 0.138
• hipred: Y
• hipred_score: 0.567
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zyx
• Phenotype: normal phenotype; cellular phenotype

Gene ontology

• Biological process: cell-matrix adhesion;transforming growth factor beta receptor signaling pathway;integrin-mediated signaling pathway;cell-cell signaling;viral process;stress fiber assembly;regulation of inflammatory response;cellular response to interferon-gamma
• Cellular component: stress fiber;nucleus;cytosol;cell-cell adherens junction;focal adhesion;phagocytic vesicle
• Molecular function: RNA binding;protein binding;metal ion binding