SDK2

sidekick cell adhesion molecule 2, the group of Fibronectin type III domain containing|I-set domain containing

Basic information

Region (hg38): 17:73334383-73644445

Links

ENSG00000069188 ∙ NCBI:54549 ∙ OMIM:607217 ∙ HGNC:19308 ∙ Uniprot:Q58EX2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDK2 gene.

• Inborn genetic diseases (101 variants)
• not provided (15 variants)
• See cases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDK2 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				7	3	10
missense			103	3	2	108
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	103	10	5

Variants in SDK2

This is a list of pathogenic ClinVar variants found in the SDK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-73338612-A-G		not specified	Uncertain significance (Feb 13, 2024)
17-73338651-C-T		SDK2-related disorder	Likely benign (May 05, 2023)
17-73338652-G-A		not specified	Uncertain significance (Apr 12, 2022)
17-73338697-G-T		not specified	Uncertain significance (Jun 29, 2022)
17-73338723-C-T		See cases	Uncertain significance (Sep 12, 2019)
17-73338730-G-C		not specified	Uncertain significance (Nov 17, 2022)
17-73338734-G-T			Likely benign (Jun 01, 2022)
17-73338805-T-G		not specified	Uncertain significance (Nov 07, 2022)
17-73338819-C-G		not specified	Uncertain significance (Sep 22, 2023)
17-73348594-C-G		SDK2-related disorder	Likely benign (Feb 26, 2022)
17-73348650-A-G		SDK2-related disorder	Likely benign (Aug 01, 2019)
17-73348661-C-T		not specified	Uncertain significance (May 05, 2023)
17-73348683-A-C		not specified	Uncertain significance (Nov 12, 2021)
17-73350240-G-T		not specified	Uncertain significance (Dec 12, 2023)
17-73350277-C-T		not specified	Uncertain significance (Nov 01, 2022)
17-73350278-G-A			Likely benign (Apr 01, 2022)
17-73350340-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-73350341-G-T		not specified	Uncertain significance (Sep 29, 2023)
17-73350374-C-G		SDK2-related disorder	Benign (Apr 15, 2019)
17-73350655-T-A		not specified	Uncertain significance (Jun 22, 2021)
17-73350681-C-G		not specified	Uncertain significance (Apr 07, 2022)
17-73350782-C-T		not specified	Uncertain significance (Feb 10, 2022)
17-73352479-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-73352507-G-A		SDK2-related disorder	Likely benign (Apr 26, 2019)
17-73352610-T-A		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDK2	protein_coding	protein_coding	ENST00000392650	45	309706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00414	0.996	125605	0	38	125643	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.68	1055	1.33e+3	0.793	0.0000893	13858
Missense in Polyphen		449	604.05	0.74331		6215
Synonymous	-0.526	588	572	1.03	0.0000423	4413
Loss of Function	7.11	27	106	0.255	0.00000534	1165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000208	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.0000722	0.0000653
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adhesion molecule that promotes lamina-specific synaptic connections in the retina and is specifically required for the formation of neuronal circuits that detect motion. Acts by promoting formation of synapses between two specific retinal cell types: the retinal ganglion cells W3B-RGCs and the excitatory amacrine cells VG3-ACs. Formation of synapses between these two cells plays a key role in detection of motion. Promotes synaptic connectivity via homophilic interactions. {ECO:0000250|UniProtKB:Q6V4S5}.
• Pathway: SDK interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -2.47
• rvis_percentile_EVS: 0.98

Haploinsufficiency Scores

• pHI: 0.413
• hipred: Y
• hipred_score: 0.550
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.264

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdk2
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;synapse assembly;retina layer formation;cell-cell junction organization;camera-type eye photoreceptor cell differentiation
• Cellular component: plasma membrane;integral component of membrane;cell junction;synapse