STRN4

striatin 4, the group of WD repeat domain containing|Protein phosphatase 2 regulatory subunits|STRIPAK complex

Basic information

Region (hg38): 19:46719511-46746994

Links

ENSG00000090372 ∙ NCBI:29888 ∙ OMIM:614767 ∙ HGNC:15721 ∙ Uniprot:Q9NRL3 ∙ 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 STRN4 gene.

• Autosomal recessive limb-girdle muscular dystrophy type 2I (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STRN4 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				1	2	3
missense			53		1	54
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding	1		1	7	3	12
Total	1	0	56	8	6

Variants in STRN4

This is a list of pathogenic ClinVar variants found in the STRN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46720631-C-T		not specified	Uncertain significance (Jan 06, 2023)
19-46720724-C-T		not specified	Uncertain significance (Mar 07, 2024)
19-46722004-C-T		not specified	Uncertain significance (Oct 03, 2022)
19-46722019-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-46722064-C-A		not specified	Uncertain significance (Feb 27, 2023)
19-46722321-T-G		not specified	Uncertain significance (Nov 07, 2022)
19-46722818-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-46722821-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-46722822-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-46722832-C-T			Benign (Jan 19, 2018)
19-46722857-A-G		not specified	Uncertain significance (Nov 18, 2022)
19-46722858-T-C			Benign (Mar 30, 2018)
19-46722881-G-A		not specified	Uncertain significance (May 10, 2024)
19-46722912-C-T		not specified	Uncertain significance (Oct 12, 2021)
19-46722920-G-T		not specified	Uncertain significance (Apr 06, 2024)
19-46723174-G-A		not specified	Uncertain significance (Jan 02, 2024)
19-46723207-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-46723276-C-G		not specified	Uncertain significance (May 09, 2022)
19-46724827-A-G		not specified	Uncertain significance (Nov 22, 2023)
19-46724828-T-C		not specified	Uncertain significance (Apr 04, 2024)
19-46724835-G-C		not specified	Uncertain significance (Dec 03, 2021)
19-46724906-T-C		not specified	Uncertain significance (Feb 14, 2023)
19-46724915-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-46724928-C-T		not specified	Likely benign (Aug 21, 2023)
19-46725368-A-T		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STRN4	protein_coding	protein_coding	ENST00000391910	17	27488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00624	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	328	467	0.702	0.0000306	4935
Missense in Polyphen		131	227.6	0.57557		2299
Synonymous	-0.282	211	206	1.02	0.0000152	1560
Loss of Function	4.65	4	32.7	0.122	0.00000148	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000362	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds calmodulin in a calcium dependent manner. May function as scaffolding or signaling protein.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.220
• rvis_EVS: -1.29
• rvis_percentile_EVS: 5.08

Haploinsufficiency Scores

• pHI: 0.222
• hipred: Y
• hipred_score: 0.775
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Strn4

Gene ontology

• Biological process: biological_process
• Cellular component: cytoplasm;membrane;dendrite;dendritic spine;FAR/SIN/STRIPAK complex
• Molecular function: protein binding;calmodulin binding;protein-containing complex binding;protein phosphatase 2A binding;armadillo repeat domain binding