SCYL3

protein-coding

SCY1 like pseudokinase 3, the group of SCY1 like pseudokinases

Gene summary

This gene encodes a protein with a kinase domain and four HEAT repeats. The encoded protein interacts with the C-terminal domain of ezrin, an ERM protein, and may play a role in cell adhesion and migration. Alternative splicing results in multiple transcript variants encoding multiple isoforms. [provided by RefSeq, Jun 2012]

MANE transcript

NM_020423.7

Inheritance

—

ClinVar variants

U:79B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr1:169,849,631-169,894,267

External References & Databases

Ensembl (ENSG00000000457)

Transcript & Mutation Effects

hg38 • Region Span ~44.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCYL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020423.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	4 clinvar		9
missense			73 clinvar	2 clinvar		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	79	6	0	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020423.7	RefSeq	NP_065156.5	12	MANE Select
ENST00000367771.11	Ensembl	ENSP00000356745.5	12	MANE Select
NM_181093.4	RefSeq	NP_851607.2	13	Standard
ENST00000367770.5	Ensembl	ENSP00000356744.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
cell migration

Molecular Function

protein binding
ATP binding
kinase activity

Cellular Component

cytoplasm
Golgi apparatus
lamellipodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367772
Coding exons: 13
Length: 44637
Individuals with no LoFs: 125713
Homozygous LoFs: 0
Heterozygous LoFs: 35
Defined: 125748
p: 0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.985	332	386	0.859	0.0000192	4834
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.00032	0.00030	rare
East Asian	0.00039	0.00038	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000066	0.000065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.958

Gene Damage Prediction

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