STRADA

STE20 related adaptor alpha

Basic information

Region (hg38): 17:63682335-63741986

Links

ENSG00000266173 ∙ NCBI:92335 ∙ OMIM:608626 ∙ HGNC:30172 ∙ Uniprot:Q7RTN6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• polyhydramnios, megalencephaly, and symptomatic epilepsy (Strong), mode of inheritance: AR
• polyhydramnios, megalencephaly, and symptomatic epilepsy (Strong), mode of inheritance: AR
• polyhydramnios, megalencephaly, and symptomatic epilepsy (Supportive), mode of inheritance: AR
• polyhydramnios, megalencephaly, and symptomatic epilepsy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Polyhydramnios, megalencephaly, and symptomatic epilepsy	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Endocrine; Neurologic; Obstetric; Renal	17522105
The condition can affect the pregnancy (due to polyhydramnios) with the affected individual

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STRADA gene.

• Polyhydramnios, megalencephaly, and symptomatic epilepsy (326 variants)
• not provided (15 variants)
• Inborn genetic diseases (10 variants)
• not specified (4 variants)
• intellectual deficiency;Polyhydramnios;Epilepsy (1 variants)
• Childhood epilepsy with centrotemporal spikes (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STRADA 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			3	70	1	74
missense			144	3	1	148
nonsense	5		2	1		8
start loss						0
frameshift	4		4			8
inframe indel			4			4
splice donor/acceptor (+/-2bp)		3				3
splice region			8	11		19
non coding			10	51	4	65
Total	9	3	167	125	6

Highest pathogenic variant AF is 0.00000658

Variants in STRADA

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

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

Position	Type	Phenotype	Significance	ClinVar
17-63685671-G-C			Benign (Jun 19, 2021)
17-63685825-T-C			Benign (Nov 12, 2018)
17-63685848-A-G			Benign (Jun 19, 2021)
17-63688315-T-C			Benign (Jun 20, 2021)
17-63688530-A-C		MAP3K3-related disorder	Likely benign (Jan 23, 2024)
17-63688813-A-G		not specified	Uncertain significance (Jul 05, 2023)
17-63688839-C-T		not specified	Uncertain significance (Apr 14, 2022)
17-63688843-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-63688851-G-A			Benign (Apr 16, 2018)
17-63689097-T-G			Benign (Jun 19, 2021)
17-63689520-C-A			Benign (Jun 19, 2021)
17-63689571-G-A		not specified	Uncertain significance (Dec 05, 2022)
17-63689605-C-T			Benign (Feb 20, 2018)
17-63689632-G-C		not specified	Uncertain significance (Nov 16, 2021)
17-63689638-G-A		not specified	Uncertain significance (Aug 08, 2023)
17-63689640-G-A		not specified	Uncertain significance (Jan 26, 2023)
17-63689690-A-G		not specified	Uncertain significance (Jan 03, 2024)
17-63689721-A-G		not specified	Uncertain significance (Nov 09, 2022)
17-63690291-G-A		not specified	Uncertain significance (Jan 02, 2024)
17-63690320-G-A		not specified	Uncertain significance (Jul 19, 2023)
17-63691202-C-A		not specified	Uncertain significance (Aug 09, 2021)
17-63691212-C-G		Verrucous hemangioma • Verrucous venous malformation	Pathogenic/Likely pathogenic (Aug 27, 2023)
17-63691733-G-C		not specified	Uncertain significance (Oct 13, 2023)
17-63691819-G-A		not specified	Uncertain significance (Jun 29, 2022)
17-63691851-G-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STRADA	protein_coding	protein_coding	ENST00000336174	12	39139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000448	0.991	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	190	257	0.739	0.0000145	2830
Missense in Polyphen		70	102.45	0.68323		1150
Synonymous	0.509	96	103	0.936	0.00000615	844
Loss of Function	2.36	13	26.0	0.501	0.00000151	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000330	0.000323
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000381	0.000381
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pseudokinase which, in complex with CAB39/MO25 (CAB39/MO25alpha or CAB39L/MO25beta), binds to and activates STK11/LKB1. Adopts a closed conformation typical of active protein kinases and binds STK11/LKB1 as a pseudosubstrate, promoting conformational change of STK11/LKB1 in an active conformation. {ECO:0000269|PubMed:12805220, ECO:0000269|PubMed:14517248, ECO:0000269|PubMed:19892943}.
• Disease: DISEASE: Note=A homozygous 7-kb deletion involving STRADA is a cause of a syndrome characterized by polyhydramnios, megalencephaly and symptomatic epilepsy.
• Pathway: mTOR signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Signal Transduction;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;LKB1 signaling events (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.801
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.756
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.775

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Strada

Gene ontology

• Biological process: MAPK cascade;protein phosphorylation;protein export from nucleus;cell cycle arrest;signal transduction by protein phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;neuron projection morphogenesis;positive regulation of protein serine/threonine kinase activity
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;kinase binding;protein kinase activator activity;protein serine/threonine kinase activator activity