SHANK3

Chr 22AD

SH3 and multiple ankyrin repeat domains 3

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

SHANK3 encodes a multidomain scaffold protein that connects neurotransmitter receptors, ion channels, and membrane proteins to the actin cytoskeleton in postsynaptic densities and regulates synapse formation and dendritic spine maturation. Loss-of-function mutations cause autosomal dominant Phelan-McDermid syndrome (22q13.3 deletion syndrome) characterized by autism spectrum disorder, intellectual disability, and neurological symptoms, as well as schizophrenia type 15. The protein is highly intolerant to loss-of-function variants, indicating haploinsufficiency as the primary disease mechanism.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismADLOEUF 0.122 OMIM phenotypes
Clinical SummarySHANK3
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Gene-Disease Validity (ClinGen)
Phelan-McDermid syndrome · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
5 active or recruiting trials — potential therapeutic options may be available

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 OE0.04 (0.010.12)
00.351.4
Missense OE0.65 (0.600.69)
00.61.4
Synonymous OE1.21
01.21.6
LoF obs/exp: 2 / 51.0Missense obs/exp: 571 / 884.2Syn Z: -3.40
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongSHANK3-related Phelan-Mcdermid syndromeLOFAD
DN
0.3693th %ile
GOF
0.5661th %ile
LOF
0.82top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 1 literature citation · LOEUF 0.12

Literature Evidence

LOFAnalysis of single SHANK3 mRNA molecules in neurons derived from an autistic individual heterozygous for SHANK3 indicated that while the number of SHANK3 mRNA transcripts remained comparable with control levels in the cell soma, there was a 50% reduction within neuronal processes, suggesting that loPMID:30064494

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

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.

3D Protein StructureAlphaFold
Clinical Literature
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