SCYL3

SCY1 like pseudokinase 3, the group of SCY1 like pseudokinases

Basic information

Region (hg38): 1:169849631-169894267

Links

ENSG00000000457 ∙ NCBI:57147 ∙ OMIM:608192 ∙ HGNC:19285 ∙ Uniprot:Q8IZE3 ∙ 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 SCYL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCYL3 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				2		2
missense			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	34	5	1

Variants in SCYL3

This is a list of pathogenic ClinVar variants found in the SCYL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-169851821-G-A			Likely benign (Feb 01, 2023)
1-169851914-A-C			Benign (Jul 06, 2018)
1-169853751-C-G		not specified	Uncertain significance (Nov 09, 2024)
1-169854293-A-G		not specified	Uncertain significance (Dec 06, 2021)
1-169854309-C-G		not specified	Uncertain significance (Dec 21, 2022)
1-169854359-C-T		not specified	Uncertain significance (Aug 08, 2022)
1-169854367-A-G		not specified	Uncertain significance (Dec 09, 2023)
1-169854470-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-169854472-C-T		not specified	Uncertain significance (Dec 17, 2023)
1-169854495-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-169854533-C-T		not specified	Likely benign (Nov 19, 2024)
1-169854551-C-A		not specified	Uncertain significance (Sep 16, 2021)
1-169854554-C-T		not specified	Likely benign (Nov 15, 2023)
1-169854566-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-169854607-T-G		not specified	Uncertain significance (Aug 16, 2022)
1-169854650-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-169854690-G-C		not specified	Uncertain significance (Feb 16, 2023)
1-169854701-T-C		not specified	Uncertain significance (Nov 22, 2024)
1-169854793-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-169854850-G-C		not specified	Uncertain significance (May 09, 2024)
1-169854877-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-169854916-T-C		not specified	Uncertain significance (Dec 27, 2023)
1-169855800-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-169855858-C-T		not specified	Likely benign (Aug 12, 2021)
1-169855868-A-G		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCYL3	protein_coding	protein_coding	ENST00000367772	13	44637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.282	0.718	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.985	332	386	0.859	0.0000192	4834
Missense in Polyphen		86	122.84	0.70007		1592
Synonymous	0.708	136	147	0.926	0.00000768	1448
Loss of Function	4.16	8	34.3	0.233	0.00000172	442

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000389	0.000388
Ashkenazi Jewish	0.000321	0.000298
East Asian	0.000387	0.000381
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.000387	0.000381
South Asian	0.0000656	0.0000653
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulating cell adhesion/migration complexes in migrating cells. {ECO:0000269|PubMed:12651155}.

Recessive Scores

• pRec: 0.0750

Intolerance Scores

• loftool: 0.841
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.71

Haploinsufficiency Scores

• pHI: 0.191
• hipred: Y
• hipred_score: 0.704
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scyl3
• Phenotype: growth/size/body region phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein phosphorylation;cell migration
• Cellular component: cytoplasm;Golgi apparatus;lamellipodium
• Molecular function: protein binding;ATP binding;kinase activity