SHANK3

Chr 22AD

SH3 and multiple ankyrin repeat domains 3

Also known as: DEL22q13.3, PROSAP2, PSAP2, SCZD15, SPANK-2

This gene is a member of the Shank gene family. Shank proteins are multidomain scaffold proteins of the postsynaptic density that connect neurotransmitter receptors, ion channels, and other membrane proteins to the actin cytoskeleton and G-protein-coupled signaling pathways. Shank proteins also play a role in synapse formation and dendritic spine maturation. Mutations in this gene are a cause of autism spectrum disorder (ASD), which is characterized by impairments in social interaction and communication, and restricted behavioral patterns and interests. Mutations in this gene also cause schizophrenia type 15, and are a major causative factor in the neurological symptoms of 22q13.3 deletion syndrome, which is also known as Phelan-McDermid syndrome. Additional isoforms have been described for this gene but they have not yet been experimentally verified. [provided by RefSeq, Mar 2012]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

{Schizophrenia 15}MIM #613950
AD
Phelan-McDermid syndromeMIM #606232
AD

Clinical highlights

Gene-disease validity (ClinGen)
Phelan-McDermid syndrome · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
6
Active trials
160
Pubs (1 yr)
P/LP submissions
P/LP missense
0.12
LOEUF· LoF intol.
LOF
Mechanism· G2P
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GeneReview available — SHANK3
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint?
0.12LOEUF
pLI 1.000
Z-score 6.36
OE 0.04 (0.010.12)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
3.74Z-score
OE missense 0.65 (0.600.69)
571 obs / 884.2 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.04 (0.010.12)
00.351.4
Missense OE?0.65 (0.600.69)
00.61.4
Synonymous OE?1.21
01.21.6
LoF obs/exp: 2 / 51.0Missense obs/exp: 571 / 884.2Syn Z: -3.40

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SHANK3 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov