SDK1

sidekick cell adhesion molecule 1, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 7:3301251-4269000

Links

ENSG00000146555 ∙ NCBI:221935 ∙ OMIM:607216 ∙ HGNC:19307 ∙ Uniprot:Q7Z5N4 ∙ 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 SDK1 gene.

• Inborn genetic diseases (151 variants)
• not provided (34 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDK1 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	10	9	20
missense			146	9	6	161
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	148	19	15

Variants in SDK1

This is a list of pathogenic ClinVar variants found in the SDK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-3301594-G-C		not specified	Uncertain significance (Oct 14, 2023)
7-3301602-C-T		not specified	Uncertain significance (Jun 29, 2023)
7-3301644-C-G		not specified	Likely benign (Apr 13, 2022)
7-3301672-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-3301678-C-A		not specified	Uncertain significance (Aug 22, 2023)
7-3301678-C-T		not specified	Uncertain significance (Aug 22, 2023)
7-3301726-A-C		not specified	Uncertain significance (Jun 24, 2022)
7-3301728-C-A		not specified	Uncertain significance (Aug 09, 2021)
7-3301741-G-C		not specified	Uncertain significance (Jul 11, 2023)
7-3301753-A-C		not specified	Uncertain significance (Oct 20, 2021)
7-3301754-G-T		not specified	Uncertain significance (Jul 05, 2022)
7-3301755-A-C		not specified	Uncertain significance (Oct 20, 2021)
7-3301768-A-C		not specified	Uncertain significance (Oct 20, 2021)
7-3301788-T-G		not specified	Uncertain significance (Aug 11, 2021)
7-3301792-G-T		not specified	Uncertain significance (Jul 21, 2021)
7-3301797-C-T		not specified	Uncertain significance (Nov 09, 2021)
7-3301811-G-C		not specified	Uncertain significance (Dec 18, 2023)
7-3301818-C-A		not specified	Uncertain significance (Oct 27, 2022)
7-3301829-C-G			Likely benign (Jan 01, 2023)
7-3301840-C-T		not specified	Uncertain significance (Feb 14, 2024)
7-3301849-C-G		not specified	Uncertain significance (Jun 23, 2021)
7-3301873-C-T		not specified	Uncertain significance (Aug 14, 2023)
7-3619145-C-T		not specified	Uncertain significance (Jul 20, 2021)
7-3619160-C-T		not specified	Uncertain significance (Jul 13, 2022)
7-3619185-A-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDK1	protein_coding	protein_coding	ENST00000404826	45	967553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000416	1.00	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.10	1558	1.34e+3	1.16	0.0000896	14119
Missense in Polyphen		368	388.16	0.94806		3911
Synonymous	-6.61	803	597	1.34	0.0000471	4621
Loss of Function	6.70	31	105	0.295	0.00000499	1208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00136	0.00136
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.0000503	0.0000462
European (Non-Finnish)	0.000229	0.000202
Middle Eastern	0.000273	0.000272
South Asian	0.000201	0.000196
Other	0.000506	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adhesion molecule that promotes lamina-specific synaptic connections in the retina. Expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions. {ECO:0000250|UniProtKB:Q8AV58}.
• Pathway: SDK interactions;Cell-cell junction organization;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.433
• rvis_EVS: -4.63
• rvis_percentile_EVS: 0.08

Haploinsufficiency Scores

• pHI: 0.239
• hipred: Y
• hipred_score: 0.554
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdk1

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;synapse assembly;retina layer formation;cell-cell junction organization;behavioral response to cocaine;regulation of dendritic spine development
• Cellular component: plasma membrane;integral component of membrane;cell junction;synapse
• Molecular function: identical protein binding