SDK1

Chr 7

sidekick cell adhesion molecule 1

NCBI Gene: 221935ENSG00000146555UniProt: Q7Z5N4

The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

337
ClinVar variants
5
Pathogenic / LP
0.00
pLI score
1
Active trials
Clinical Summary— SDK1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.29) despite low pLI — interpret in context.
📋
ClinVar Variants
5 Pathogenic / Likely Pathogenic· 303 VUS of 337 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.40LOEUF
pLI 0.000
Z-score 6.70
OE 0.29 (0.22–0.40)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-2.10Z-score
OE missense 1.16 (1.11–1.21)
1558 obs / 1341.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.29 (0.22–0.40)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.16 (1.11–1.21)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.34
0≤1.21.6
LoF obs/exp: 31 / 105.1Missense obs/exp: 1558 / 1341.5Syn Z: -6.61

ClinVar Variant Classifications

337 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5
VUS303
Likely Benign29
5
Pathogenic
303
VUS
29
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
5
0
5
Likely Pathogenic
0
0
0
0
0
VUS
0
299
4
0
303
Likely Benign
0
15
2
12
29
Benign
0
0
0
0
0
Total03141112337

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SDK1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genome-wide methylation patterns in Marfan syndrome.
van Andel MM et al.·Clin Epigenetics
2021
Clustering by phenotype and genome-wide association study in autism.
Narita A et al.·Transl Psychiatry
2020
Androgen-responsive serum response factor target genes regulate prostate cancer cell migration.
Verone AR et al.·Carcinogenesis
2013
Longitudinal genome-wide methylation study of PTSD treatment using prolonged exposure and hydrocortisone.
Yang R et al.·Transl Psychiatry
2021Natural history
Differentially expressed genes associated with high metabolic tumor volume served as diagnostic markers and potential therapeutic targets for pancreatic cancer.
Kim BG et al.·J Transl Med
2024
Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing.
Mäki-Nevala S et al.·Lung
2016
Exposure to childhood abuse is associated with human sperm DNA methylation.
Roberts AL et al.·Transl Psychiatry
2018
Novel loci for ocular axial length identified through extreme-phenotype genome-wide association study in Chinese populations.
Han X et al.·Br J Ophthalmol
2024Meta-analysis
Histologic features and genomic alterations of primary colorectal adenocarcinoma predict growth patterns of liver metastasis.
Wu JB et al.·World J Gastroenterol
2019
A web-based survey on various symptoms of computer vision syndrome and the genetic understanding based on a multi-trait genome-wide association study.
Yoshimura K et al.·Sci Rep
2021
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Non-small Cell Lung CancerEGFR Gene MutationEGFR-TKI Resistant Mutation

Nintedanib Plus EGFR TKI In EGFR-mutated Non-small Cell Lung Cancer Patients

RECRUITING
NCT06071013Phase PHASE1, PHASE2China Medical University HospitalStarted 2024-02-23
Nintedanib, gefitinib, erlotinib, afatinib, osimertinib

External Resources

Links to major genomics databases and tools